From 6b519beb621845900351785592f3a8b394b9d589 Mon Sep 17 00:00:00 2001
From: smitdave <smitdave@users.noreply.github.com>
Date: Tue, 16 Jan 2024 20:34:49 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20dd-harp/?=
 =?UTF-8?q?exDE@fd48f1bbaf5101c9b6ffdff88ffd5d35e2e65669=20=F0=9F=9A=80?=
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Content-Type: text/plain; charset=UTF-8
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---
 articles/adult_RM.html                        |   3 +-
 .../figure-html/unnamed-chunk-14-1.png        | Bin 140252 -> 141478 bytes
 pkgdown.yml                                   |   2 +-
 reference/Exposure.html                       |  27 +++-
 reference/F_foi.html                          |  30 +++-
 reference/F_foi.nb.html                       |   8 +-
 reference/F_foi.pois.html                     |   8 +-
 reference/Transmission.html                   |   4 +-
 reference/compute_NI.html                     |   2 +-
 reference/compute_NI_ix.html                  |   2 +-
 reference/compute_fqM.html                    |   2 +-
 reference/compute_fqM_ix.html                 |   2 +-
 reference/compute_fqZ.html                    |   2 +-
 reference/compute_fqZ_ix.html                 |   2 +-
 reference/compute_terms.cohort.html           |   2 +-
 reference/compute_terms.html                  |   2 +-
 reference/compute_terms.human.html            |   2 +-
 reference/compute_terms.na.html               |   2 +-
 reference/compute_terms.xde.html              |   2 +-
 reference/compute_terms_steady.html           |   2 +-
 reference/compute_vars_aqua.html              | 132 +++++++++++++++++
 reference/compute_vars_cohort.html            | 136 ++++++++++++++++++
 reference/compute_vars_full.html              | 132 +++++++++++++++++
 reference/compute_vars_human.html             | 132 +++++++++++++++++
 reference/compute_vars_mosy.html              | 133 +++++++++++++++++
 reference/index.html                          |  47 ++++--
 reference/travel_malaria.html                 |   2 +-
 reference/xde_lines_EIR.html                  |  14 +-
 reference/xde_lines_PR.html                   |  14 +-
 reference/xde_lines_X_SIS.html                |   6 +-
 reference/xde_lines_aEIR.html                 |  20 +--
 reference/xde_plot_EIR.html                   |  13 +-
 reference/xde_plot_PR.html                    |  13 +-
 reference/xde_plot_aEIR.html                  |  13 +-
 search.json                                   |   2 +-
 sitemap.xml                                   |  15 ++
 36 files changed, 857 insertions(+), 73 deletions(-)
 create mode 100644 reference/compute_vars_aqua.html
 create mode 100644 reference/compute_vars_cohort.html
 create mode 100644 reference/compute_vars_full.html
 create mode 100644 reference/compute_vars_human.html
 create mode 100644 reference/compute_vars_mosy.html

diff --git a/articles/adult_RM.html b/articles/adult_RM.html
index 62472512..cb9be1bd 100644
--- a/articles/adult_RM.html
+++ b/articles/adult_RM.html
@@ -285,7 +285,8 @@ <h3 id="the-long-way">The long way<a class="anchor" aria-label="anchor" href="#t
 <p>We and set the indices with <code><a href="../reference/make_indices.html">exDE::make_indices</a></code>.</p>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">params</span><span class="op">$</span><span class="va">max_ix</span> <span class="op">=</span> <span class="fl">0</span> </span>
-<span><span class="va">params</span> <span class="op">=</span> <span class="fu"><a href="../reference/make_indices.html">make_indices</a></span><span class="op">(</span><span class="va">params</span><span class="op">)</span></span></code></pre></div>
+<span><span class="va">params</span> <span class="op">=</span> <span class="fu"><a href="../reference/make_indices.html">make_indices</a></span><span class="op">(</span><span class="va">params</span><span class="op">)</span></span>
+<span><span class="va">params</span><span class="op">$</span><span class="va">nHosts</span> <span class="op">=</span> <span class="fl">0</span> </span></code></pre></div>
 <p>Then we can set up the initial conditions vector and use
 <code><a href="https://rdrr.io/pkg/deSolve/man/ode.html" class="external-link">deSolve::ode</a></code> to solve the model. Normally these values
 would be computed within <code><a href="../reference/xDE_diffeqn.html">exDE::xDE_diffeqn</a></code>. Here, we set up
diff --git a/articles/vc_lemenach_files/figure-html/unnamed-chunk-14-1.png b/articles/vc_lemenach_files/figure-html/unnamed-chunk-14-1.png
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diff --git a/pkgdown.yml b/pkgdown.yml
index bf989019..6d39c47a 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -15,7 +15,7 @@ articles:
   modularity: modularity.html
   spat_metric: spat_metric.html
   vc_lemenach: vc_lemenach.html
-last_built: 2024-01-15T19:48Z
+last_built: 2024-01-16T20:32Z
 urls:
   reference: https://dd-harp.github.io/exDE/reference
   article: https://dd-harp.github.io/exDE/articles
diff --git a/reference/Exposure.html b/reference/Exposure.html
index 862390ee..7f7e97d4 100644
--- a/reference/Exposure.html
+++ b/reference/Exposure.html
@@ -1,5 +1,15 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A model for exposure. The function F_b must be define"><title>A model for exposure. The function F_b must be define — Exposure • exDE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="A model for exposure. The function F_b must be define — Exposure"><meta property="og:description" content="A model for exposure. The function F_b must be define"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function translates the local daily entomological
+inoculation rate (dEIR), computed as one of the transmission terms
+into a measure of the daily force of infection (dFoI). The daily FoI
+is the sum of two terms: 1) a function F_foi computes the local dFoI;
+2) a function travel_malaria that computes the FoI resulting from
+exposure while traveling."><title>Exposure and Infection — Exposure • exDE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Exposure and Infection — Exposure"><meta property="og:description" content="This function translates the local daily entomological
+inoculation rate (dEIR), computed as one of the transmission terms
+into a measure of the daily force of infection (dFoI). The daily FoI
+is the sum of two terms: 1) a function F_foi computes the local dFoI;
+2) a function travel_malaria that computes the FoI resulting from
+exposure while traveling."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <![endif]--></head><body>
@@ -70,13 +80,18 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>A model for exposure. The function <code>F_b</code> must be define</h1>
+      <img src="" class="logo" alt=""><h1>Exposure and Infection</h1>
       <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/exposure.R" class="external-link"><code>R/exposure.R</code></a></small>
       <div class="d-none name"><code>Exposure.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
-    <p>A model for exposure. The function <code>F_b</code> must be define</p>
+    <p>This function translates the local daily entomological
+inoculation rate (dEIR), computed as one of the transmission terms
+into a measure of the daily force of infection (dFoI). The daily FoI
+is the sum of two terms: 1) a function <a href="F_foi.html">F_foi</a> computes the local dFoI;
+2) a function <a href="travel_malaria.html">travel_malaria</a> that computes the FoI resulting from
+exposure while traveling.</p>
     </div>
 
     <div class="section level2">
@@ -91,18 +106,18 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt>y</dt>
-<dd><p>the variables</p></dd>
+<dd><p>the state variables</p></dd>
 
 
 <dt>pars</dt>
-<dd><p>a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p></dd>
+<dd><p>the model object as a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
     
 
-<p><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p>
+<p>the function modifies <strong>pars</strong> and returns it: the computed FoI are stored as <code>pars$FoI</code></p>
 
 
     </div>
diff --git a/reference/F_foi.html b/reference/F_foi.html
index 5f14b45c..96e12970 100644
--- a/reference/F_foi.html
+++ b/reference/F_foi.html
@@ -1,5 +1,17 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This method dispatches on the type of pars$FOIpar."><title>A model for exposure — F_foi • exDE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="A model for exposure — F_foi"><meta property="og:description" content="This method dispatches on the type of pars$FOIpar."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function compute the daily local FoI as a function
+of the daily EIR and effects of partial immunity.
+It is computed based on a probabilistic model of exposure and
+possibly including environmental heterogeneity. If a model of human / host
+infection has terms that describe partial immunity, e.g. affecting
+pre-erythrocytic immunity to malaria called by F_b, those effects are implemented here.
+The method dispatches on the type of pars$FOIpar."><title>A model for daily FoI as a function of the daily EIR. — F_foi • exDE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="A model for daily FoI as a function of the daily EIR. — F_foi"><meta property="og:description" content="This function compute the daily local FoI as a function
+of the daily EIR and effects of partial immunity.
+It is computed based on a probabilistic model of exposure and
+possibly including environmental heterogeneity. If a model of human / host
+infection has terms that describe partial immunity, e.g. affecting
+pre-erythrocytic immunity to malaria called by F_b, those effects are implemented here.
+The method dispatches on the type of pars$FOIpar."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -70,13 +82,19 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>A model for exposure</h1>
+      <img src="" class="logo" alt=""><h1>A model for daily FoI as a function of the daily EIR.</h1>
       <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/exposure.R" class="external-link"><code>R/exposure.R</code></a></small>
       <div class="d-none name"><code>F_foi.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
-    <p>This method dispatches on the type of <code>pars$FOIpar</code>.</p>
+    <p>This function compute the daily local FoI as a function
+of the daily EIR and effects of partial immunity.
+It is computed based on a probabilistic model of exposure and
+possibly including environmental heterogeneity. If a model of human / host
+infection has terms that describe partial immunity, <em>e.g.</em> affecting
+pre-erythrocytic immunity to malaria called by <a href="F_b.html">F_b</a>, those effects are implemented here.
+The method dispatches on the type of <code>pars$FOIpar</code>.</p>
     </div>
 
     <div class="section level2">
@@ -87,7 +105,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
     <dl><dt>eir</dt>
-<dd><p>the daily eir</p></dd>
+<dd><p>the daily eir for each stratum</p></dd>
 
 
 <dt>b</dt>
@@ -95,14 +113,14 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt>pars</dt>
-<dd><p>a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p></dd>
+<dd><p>the model object as a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p></dd>
 
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
     
 
-<p>see help pages for specific methods</p>
+<p>the daily, local force of infection as a <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> vector</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/F_foi.nb.html b/reference/F_foi.nb.html
index 1b8e6f23..e8eda18c 100644
--- a/reference/F_foi.nb.html
+++ b/reference/F_foi.nb.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Implements F_foi for a negative binomial model"><title>Null human population births — F_foi.nb • exDE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Null human population births — F_foi.nb"><meta property="og:description" content="Implements F_foi for a negative binomial model"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Implements F_foi for a negative binomial model"><title>The daily FoI as a function of the daily EIR under a negative binomial model of exposure. — F_foi.nb • exDE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="The daily FoI as a function of the daily EIR under a negative binomial model of exposure. — F_foi.nb"><meta property="og:description" content="Implements F_foi for a negative binomial model"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -70,7 +70,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Null human population births</h1>
+      <img src="" class="logo" alt=""><h1>The daily FoI as a function of the daily EIR under a negative binomial model of exposure.</h1>
       <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/exposure.R" class="external-link"><code>R/exposure.R</code></a></small>
       <div class="d-none name"><code>F_foi.nb.Rd</code></div>
     </div>
@@ -88,7 +88,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
     <dl><dt>eir</dt>
-<dd><p>the daily eir</p></dd>
+<dd><p>the daily eir for each stratum</p></dd>
 
 
 <dt>b</dt>
@@ -96,7 +96,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt>pars</dt>
-<dd><p>a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p></dd>
+<dd><p>the model object as a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p></dd>
 
 </dl></div>
     <div class="section level2">
diff --git a/reference/F_foi.pois.html b/reference/F_foi.pois.html
index 14de6dfa..d6020ead 100644
--- a/reference/F_foi.pois.html
+++ b/reference/F_foi.pois.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Implements F_foi for a Poisson model"><title>Null human population births — F_foi.pois • exDE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Null human population births — F_foi.pois"><meta property="og:description" content="Implements F_foi for a Poisson model"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Implements F_foi for a Poisson model"><title>A Poisson model for the daily local FoI as a function of the daily EIR. — F_foi.pois • exDE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="A Poisson model for the daily local FoI as a function of the daily EIR. — F_foi.pois"><meta property="og:description" content="Implements F_foi for a Poisson model"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -70,7 +70,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Null human population births</h1>
+      <img src="" class="logo" alt=""><h1>A Poisson model for the daily local FoI as a function of the daily EIR.</h1>
       <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/exposure.R" class="external-link"><code>R/exposure.R</code></a></small>
       <div class="d-none name"><code>F_foi.pois.Rd</code></div>
     </div>
@@ -88,7 +88,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
     <dl><dt>eir</dt>
-<dd><p>the daily eir</p></dd>
+<dd><p>the daily eir for each stratum</p></dd>
 
 
 <dt>b</dt>
@@ -96,7 +96,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt>pars</dt>
-<dd><p>a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p></dd>
+<dd><p>the model object as a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p></dd>
 
 </dl></div>
     <div class="section level2">
diff --git a/reference/Transmission.html b/reference/Transmission.html
index 0b617d9e..07bc3cab 100644
--- a/reference/Transmission.html
+++ b/reference/Transmission.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This method dispatches on the type of pars$BFpar"><title>Compute transmission terms dynamically — Transmission • exDE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Compute transmission terms dynamically — Transmission"><meta property="og:description" content="This method dispatches on the type of pars$BFpar"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This method dispatches on the type of pars$BFpar"><title>Compute the mixing matrix and transmission terms — Transmission • exDE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Compute the mixing matrix and transmission terms — Transmission"><meta property="og:description" content="This method dispatches on the type of pars$BFpar"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -70,7 +70,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Compute transmission terms dynamically</h1>
+      <img src="" class="logo" alt=""><h1>Compute the mixing matrix and transmission terms</h1>
       <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/transmission.R" class="external-link"><code>R/transmission.R</code></a></small>
       <div class="d-none name"><code>Transmission.Rd</code></div>
     </div>
diff --git a/reference/compute_NI.html b/reference/compute_NI.html
index dc6ebae1..f9c04de3 100644
--- a/reference/compute_NI.html
+++ b/reference/compute_NI.html
@@ -73,7 +73,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Compute the NI</h1>
-      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute.R" class="external-link"><code>R/compute.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute_terms.R" class="external-link"><code>R/compute_terms.R</code></a></small>
       <div class="d-none name"><code>compute_NI.Rd</code></div>
     </div>
 
diff --git a/reference/compute_NI_ix.html b/reference/compute_NI_ix.html
index 577fa093..be42f12c 100644
--- a/reference/compute_NI_ix.html
+++ b/reference/compute_NI_ix.html
@@ -73,7 +73,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Compute NI once</h1>
-      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute.R" class="external-link"><code>R/compute.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute_terms.R" class="external-link"><code>R/compute_terms.R</code></a></small>
       <div class="d-none name"><code>compute_NI_ix.Rd</code></div>
     </div>
 
diff --git a/reference/compute_fqM.html b/reference/compute_fqM.html
index d6d0bf19..b18f4bef 100644
--- a/reference/compute_fqM.html
+++ b/reference/compute_fqM.html
@@ -73,7 +73,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Compute the fqM</h1>
-      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute.R" class="external-link"><code>R/compute.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute_terms.R" class="external-link"><code>R/compute_terms.R</code></a></small>
       <div class="d-none name"><code>compute_fqM.Rd</code></div>
     </div>
 
diff --git a/reference/compute_fqM_ix.html b/reference/compute_fqM_ix.html
index b850775a..1ea91760 100644
--- a/reference/compute_fqM_ix.html
+++ b/reference/compute_fqM_ix.html
@@ -73,7 +73,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Compute the fqM for the ith</h1>
-      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute.R" class="external-link"><code>R/compute.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute_terms.R" class="external-link"><code>R/compute_terms.R</code></a></small>
       <div class="d-none name"><code>compute_fqM_ix.Rd</code></div>
     </div>
 
diff --git a/reference/compute_fqZ.html b/reference/compute_fqZ.html
index f18aed0d..f8d213d9 100644
--- a/reference/compute_fqZ.html
+++ b/reference/compute_fqZ.html
@@ -73,7 +73,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Compute the fqZ</h1>
-      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute.R" class="external-link"><code>R/compute.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute_terms.R" class="external-link"><code>R/compute_terms.R</code></a></small>
       <div class="d-none name"><code>compute_fqZ.Rd</code></div>
     </div>
 
diff --git a/reference/compute_fqZ_ix.html b/reference/compute_fqZ_ix.html
index 98deac40..9e14fa43 100644
--- a/reference/compute_fqZ_ix.html
+++ b/reference/compute_fqZ_ix.html
@@ -73,7 +73,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Compute the fqZ for the ith</h1>
-      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute.R" class="external-link"><code>R/compute.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute_terms.R" class="external-link"><code>R/compute_terms.R</code></a></small>
       <div class="d-none name"><code>compute_fqZ_ix.Rd</code></div>
     </div>
 
diff --git a/reference/compute_terms.cohort.html b/reference/compute_terms.cohort.html
index 2446c0bd..8f2e01b3 100644
--- a/reference/compute_terms.cohort.html
+++ b/reference/compute_terms.cohort.html
@@ -73,7 +73,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Compute dynamical terms</h1>
-      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute.R" class="external-link"><code>R/compute.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute_terms.R" class="external-link"><code>R/compute_terms.R</code></a></small>
       <div class="d-none name"><code>compute_terms.cohort.Rd</code></div>
     </div>
 
diff --git a/reference/compute_terms.html b/reference/compute_terms.html
index 3975c4c8..3d0e5a8d 100644
--- a/reference/compute_terms.html
+++ b/reference/compute_terms.html
@@ -71,7 +71,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Compute dynamical terms</h1>
-      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute.R" class="external-link"><code>R/compute.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute_terms.R" class="external-link"><code>R/compute_terms.R</code></a></small>
       <div class="d-none name"><code>compute_terms.Rd</code></div>
     </div>
 
diff --git a/reference/compute_terms.human.html b/reference/compute_terms.human.html
index cbf84a8f..6e43c5ff 100644
--- a/reference/compute_terms.human.html
+++ b/reference/compute_terms.human.html
@@ -73,7 +73,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Compute dynamical terms</h1>
-      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute.R" class="external-link"><code>R/compute.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute_terms.R" class="external-link"><code>R/compute_terms.R</code></a></small>
       <div class="d-none name"><code>compute_terms.human.Rd</code></div>
     </div>
 
diff --git a/reference/compute_terms.na.html b/reference/compute_terms.na.html
index b7df334d..f6c582fe 100644
--- a/reference/compute_terms.na.html
+++ b/reference/compute_terms.na.html
@@ -75,7 +75,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Compute dynamical terms</h1>
-      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute.R" class="external-link"><code>R/compute.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute_terms.R" class="external-link"><code>R/compute_terms.R</code></a></small>
       <div class="d-none name"><code>compute_terms.na.Rd</code></div>
     </div>
 
diff --git a/reference/compute_terms.xde.html b/reference/compute_terms.xde.html
index e0284a40..050fedf9 100644
--- a/reference/compute_terms.xde.html
+++ b/reference/compute_terms.xde.html
@@ -73,7 +73,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Compute dynamical terms</h1>
-      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute.R" class="external-link"><code>R/compute.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute_terms.R" class="external-link"><code>R/compute_terms.R</code></a></small>
       <div class="d-none name"><code>compute_terms.xde.Rd</code></div>
     </div>
 
diff --git a/reference/compute_terms_steady.html b/reference/compute_terms_steady.html
index af5d6f6a..bee1c50f 100644
--- a/reference/compute_terms_steady.html
+++ b/reference/compute_terms_steady.html
@@ -73,7 +73,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="" class="logo" alt=""><h1>Compute dynamical terms</h1>
-      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute.R" class="external-link"><code>R/compute.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute_terms.R" class="external-link"><code>R/compute_terms.R</code></a></small>
       <div class="d-none name"><code>compute_terms_steady.Rd</code></div>
     </div>
 
diff --git a/reference/compute_vars_aqua.html b/reference/compute_vars_aqua.html
new file mode 100644
index 00000000..d99ee20f
--- /dev/null
+++ b/reference/compute_vars_aqua.html
@@ -0,0 +1,132 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Compute everything but the derivatives for an aquatic mosquito-only
+differential equation model"><title>Differential equation models for aquatic mosquito populations — compute_vars_aqua • exDE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Differential equation models for aquatic mosquito populations — compute_vars_aqua"><meta property="og:description" content="Compute everything but the derivatives for an aquatic mosquito-only
+differential equation model"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-adult-mosquito-dynamics">Adult Mosquito Dynamics</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-adult-mosquito-dynamics">
+    <a class="dropdown-item" href="../articles/adult_RM.html">Ross-Macdonald model</a>
+    <a class="dropdown-item" href="../articles/adult_GeRM.html">Generalized Ross-Macdonald model</a>
+  </div>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-aquatic-mosquito-dynamics">Aquatic Mosquito Dynamics</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-aquatic-mosquito-dynamics">
+    <a class="dropdown-item" href="../articles/aqua_trace.html">Trace (forced) model</a>
+    <a class="dropdown-item" href="../articles/aqua_basic.html">Basic competition model</a>
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+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-human-infection-dynamics">Human Infection Dynamics</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-human-infection-dynamics">
+    <a class="dropdown-item" href="../articles/human_sis.html">SIS model</a>
+    <a class="dropdown-item" href="../articles/human_sip.html">SIP model</a>
+    <a class="dropdown-item" href="../articles/human_hmoi.html">MoI hybrid model</a>
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+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
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+</li>
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+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+      <img src="" class="logo" alt=""><h1>Differential equation models for aquatic mosquito populations</h1>
+      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute_variables.R" class="external-link"><code>R/compute_variables.R</code></a></small>
+      <div class="d-none name"><code>compute_vars_aqua.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Compute everything but the derivatives for an aquatic mosquito-only
+differential equation model</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">compute_vars_aqua</span><span class="op">(</span><span class="va">t</span>, <span class="va">y</span>, <span class="va">pars</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <dl><dt>t</dt>
+<dd><p>current simulation time</p></dd>
+
+
+<dt>y</dt>
+<dd><p>state vector</p></dd>
+
+
+<dt>pars</dt>
+<dd><p>a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p></dd>
+
+</dl></div>
+    <div class="section level2">
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    
+
+<p><strong>pars</strong> a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p>
+
+
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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diff --git a/reference/compute_vars_cohort.html b/reference/compute_vars_cohort.html
new file mode 100644
index 00000000..c1203210
--- /dev/null
+++ b/reference/compute_vars_cohort.html
@@ -0,0 +1,136 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Compute everything but the derivatives for a human cohort
+differential equation model"><title>Differential equation models for human cohorts — compute_vars_cohort • exDE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Differential equation models for human cohorts — compute_vars_cohort"><meta property="og:description" content="Compute everything but the derivatives for a human cohort
+differential equation model"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
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+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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+    <a class="dropdown-item" href="../articles/ex_534.html">5-3-4 Spatial Example</a>
+    <a class="dropdown-item" href="../articles/spat_metric.html">Spatial Metrics</a>
+    <a class="dropdown-item" href="../articles/vc_lemenach.html">Vector Control Example</a>
+    <a class="dropdown-item" href="../articles/Contributing.html">Contributing</a>
+  </div>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-adult-mosquito-dynamics">Adult Mosquito Dynamics</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-adult-mosquito-dynamics">
+    <a class="dropdown-item" href="../articles/adult_RM.html">Ross-Macdonald model</a>
+    <a class="dropdown-item" href="../articles/adult_GeRM.html">Generalized Ross-Macdonald model</a>
+  </div>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-aquatic-mosquito-dynamics">Aquatic Mosquito Dynamics</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-aquatic-mosquito-dynamics">
+    <a class="dropdown-item" href="../articles/aqua_trace.html">Trace (forced) model</a>
+    <a class="dropdown-item" href="../articles/aqua_basic.html">Basic competition model</a>
+  </div>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-human-infection-dynamics">Human Infection Dynamics</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-human-infection-dynamics">
+    <a class="dropdown-item" href="../articles/human_sis.html">SIS model</a>
+    <a class="dropdown-item" href="../articles/human_sip.html">SIP model</a>
+    <a class="dropdown-item" href="../articles/human_hmoi.html">MoI hybrid model</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
+
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/dd-harp/exDE/">
+    <span class="fa fa-github"></span>
+     
+  </a>
+</li>
+      </ul></div>
+
+    
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+      <img src="" class="logo" alt=""><h1>Differential equation models for human cohorts</h1>
+      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute_variables.R" class="external-link"><code>R/compute_variables.R</code></a></small>
+      <div class="d-none name"><code>compute_vars_cohort.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Compute everything but the derivatives for a human cohort
+differential equation model</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">compute_vars_cohort</span><span class="op">(</span><span class="va">a</span>, <span class="va">y</span>, <span class="va">pars</span>, <span class="va">F_eir</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <dl><dt>a</dt>
+<dd><p>age of a cohort</p></dd>
+
+
+<dt>y</dt>
+<dd><p>state vector</p></dd>
+
+
+<dt>pars</dt>
+<dd><p>a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p></dd>
+
+
+<dt>F_eir</dt>
+<dd><p>a trace function that returns the eir</p></dd>
+
+</dl></div>
+    <div class="section level2">
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    
+
+<p><strong>pars</strong> a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p>
+
+
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p></p><p>Developed by Sean L. Wu, David L. Smith.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
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+
+  
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+  </body></html>
+
diff --git a/reference/compute_vars_full.html b/reference/compute_vars_full.html
new file mode 100644
index 00000000..af932e84
--- /dev/null
+++ b/reference/compute_vars_full.html
@@ -0,0 +1,132 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Compute everything but the derivatives for the generalized
+spatial differential equation model"><title>Compute other variables at time t — compute_vars_full • exDE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Compute other variables at time t — compute_vars_full"><meta property="og:description" content="Compute everything but the derivatives for the generalized
+spatial differential equation model"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+    <a class="dropdown-item" href="../articles/spat_metric.html">Spatial Metrics</a>
+    <a class="dropdown-item" href="../articles/vc_lemenach.html">Vector Control Example</a>
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+  </div>
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+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-adult-mosquito-dynamics">Adult Mosquito Dynamics</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-adult-mosquito-dynamics">
+    <a class="dropdown-item" href="../articles/adult_RM.html">Ross-Macdonald model</a>
+    <a class="dropdown-item" href="../articles/adult_GeRM.html">Generalized Ross-Macdonald model</a>
+  </div>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-aquatic-mosquito-dynamics">Aquatic Mosquito Dynamics</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-aquatic-mosquito-dynamics">
+    <a class="dropdown-item" href="../articles/aqua_trace.html">Trace (forced) model</a>
+    <a class="dropdown-item" href="../articles/aqua_basic.html">Basic competition model</a>
+  </div>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-human-infection-dynamics">Human Infection Dynamics</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-human-infection-dynamics">
+    <a class="dropdown-item" href="../articles/human_sis.html">SIS model</a>
+    <a class="dropdown-item" href="../articles/human_sip.html">SIP model</a>
+    <a class="dropdown-item" href="../articles/human_hmoi.html">MoI hybrid model</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
+
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+  <a class="external-link nav-link" href="https://github.com/dd-harp/exDE/">
+    <span class="fa fa-github"></span>
+     
+  </a>
+</li>
+      </ul></div>
+
+    
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+      <img src="" class="logo" alt=""><h1>Compute other variables at time t</h1>
+      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute_variables.R" class="external-link"><code>R/compute_variables.R</code></a></small>
+      <div class="d-none name"><code>compute_vars_full.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Compute everything but the derivatives for the generalized
+spatial differential equation model</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">compute_vars_full</span><span class="op">(</span><span class="va">t</span>, <span class="va">y</span>, <span class="va">pars</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <dl><dt>t</dt>
+<dd><p>current simulation time</p></dd>
+
+
+<dt>y</dt>
+<dd><p>state vector</p></dd>
+
+
+<dt>pars</dt>
+<dd><p>a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p></dd>
+
+</dl></div>
+    <div class="section level2">
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    
+
+<p><strong>pars</strong> a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p>
+
+
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p></p><p>Developed by Sean L. Wu, David L. Smith.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
+    </footer></div>
+
+  
+
+  
+
+  </body></html>
+
diff --git a/reference/compute_vars_human.html b/reference/compute_vars_human.html
new file mode 100644
index 00000000..9df3cb99
--- /dev/null
+++ b/reference/compute_vars_human.html
@@ -0,0 +1,132 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Compute everything but the derivatives for a human-only
+differential equation model"><title>Compute other variables at time t — compute_vars_human • exDE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Compute other variables at time t — compute_vars_human"><meta property="og:description" content="Compute everything but the derivatives for a human-only
+differential equation model"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
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+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-adult-mosquito-dynamics">Adult Mosquito Dynamics</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-adult-mosquito-dynamics">
+    <a class="dropdown-item" href="../articles/adult_RM.html">Ross-Macdonald model</a>
+    <a class="dropdown-item" href="../articles/adult_GeRM.html">Generalized Ross-Macdonald model</a>
+  </div>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-aquatic-mosquito-dynamics">Aquatic Mosquito Dynamics</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-aquatic-mosquito-dynamics">
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+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-human-infection-dynamics">Human Infection Dynamics</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-human-infection-dynamics">
+    <a class="dropdown-item" href="../articles/human_sis.html">SIS model</a>
+    <a class="dropdown-item" href="../articles/human_sip.html">SIP model</a>
+    <a class="dropdown-item" href="../articles/human_hmoi.html">MoI hybrid model</a>
+  </div>
+</li>
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+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+      <img src="" class="logo" alt=""><h1>Compute other variables at time t</h1>
+      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute_variables.R" class="external-link"><code>R/compute_variables.R</code></a></small>
+      <div class="d-none name"><code>compute_vars_human.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Compute everything but the derivatives for a human-only
+differential equation model</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">compute_vars_human</span><span class="op">(</span><span class="va">t</span>, <span class="va">y</span>, <span class="va">pars</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <dl><dt>t</dt>
+<dd><p>current simulation time</p></dd>
+
+
+<dt>y</dt>
+<dd><p>state vector</p></dd>
+
+
+<dt>pars</dt>
+<dd><p>a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p></dd>
+
+</dl></div>
+    <div class="section level2">
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    
+
+<p><strong>pars</strong> a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p>
+
+
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p></p><p>Developed by Sean L. Wu, David L. Smith.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
+    </footer></div>
+
+  
+
+  
+
+  </body></html>
+
diff --git a/reference/compute_vars_mosy.html b/reference/compute_vars_mosy.html
new file mode 100644
index 00000000..3fc77d2a
--- /dev/null
+++ b/reference/compute_vars_mosy.html
@@ -0,0 +1,133 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Compute everything but the derivatives for a mosquito-only
+differential equation model"><title>Compute other variables at time t — compute_vars_mosy • exDE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Compute other variables at time t — compute_vars_mosy"><meta property="og:description" content="Compute everything but the derivatives for a mosquito-only
+differential equation model"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
+
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
+    <a class="navbar-brand me-2" href="../index.html">exDE</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.0.0</small>
+
+    
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="active nav-item">
+  <a class="nav-link" href="../reference/index.html">Functions</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/Understanding_exDE.html">Understanding exDE</a>
+    <a class="dropdown-item" href="../articles/modularity.html">Modular Forms for Disease Dynamics</a>
+    <a class="dropdown-item" href="../articles/ex_534.html">5-3-4 Spatial Example</a>
+    <a class="dropdown-item" href="../articles/spat_metric.html">Spatial Metrics</a>
+    <a class="dropdown-item" href="../articles/vc_lemenach.html">Vector Control Example</a>
+    <a class="dropdown-item" href="../articles/Contributing.html">Contributing</a>
+  </div>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-adult-mosquito-dynamics">Adult Mosquito Dynamics</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-adult-mosquito-dynamics">
+    <a class="dropdown-item" href="../articles/adult_RM.html">Ross-Macdonald model</a>
+    <a class="dropdown-item" href="../articles/adult_GeRM.html">Generalized Ross-Macdonald model</a>
+  </div>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-aquatic-mosquito-dynamics">Aquatic Mosquito Dynamics</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-aquatic-mosquito-dynamics">
+    <a class="dropdown-item" href="../articles/aqua_trace.html">Trace (forced) model</a>
+    <a class="dropdown-item" href="../articles/aqua_basic.html">Basic competition model</a>
+  </div>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-human-infection-dynamics">Human Infection Dynamics</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-human-infection-dynamics">
+    <a class="dropdown-item" href="../articles/human_sis.html">SIS model</a>
+    <a class="dropdown-item" href="../articles/human_sip.html">SIP model</a>
+    <a class="dropdown-item" href="../articles/human_hmoi.html">MoI hybrid model</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
+
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/dd-harp/exDE/">
+    <span class="fa fa-github"></span>
+     
+  </a>
+</li>
+      </ul></div>
+
+    
+  </div>
+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+      <img src="" class="logo" alt=""><h1>Compute other variables at time t</h1>
+      <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/compute_variables.R" class="external-link"><code>R/compute_variables.R</code></a></small>
+      <div class="d-none name"><code>compute_vars_mosy.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Compute everything but the derivatives for a mosquito-only
+differential equation model</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">compute_vars_mosy</span><span class="op">(</span><span class="va">t</span>, <span class="va">y</span>, <span class="va">pars</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+    <dl><dt>t</dt>
+<dd><p>current simulation time</p></dd>
+
+
+<dt>y</dt>
+<dd><p>state vector</p></dd>
+
+
+<dt>pars</dt>
+<dd><p>a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a>
+the appropriate adult mosquito model</p></dd>
+
+</dl></div>
+    <div class="section level2">
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    
+
+<p><strong>pars</strong> a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></p>
+
+
+    </div>
+
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p></p><p>Developed by Sean L. Wu, David L. Smith.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
+    </footer></div>
+
+  
+
+  
+
+  </body></html>
+
diff --git a/reference/index.html b/reference/index.html
index 1dc92cbb..47bcff05 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -88,12 +88,7 @@ <h2 id="blood-feeding-and-transmission">Blood Feeding and Transmission<a class="
           
           <code><a href="Transmission.html">Transmission()</a></code> 
         </dt>
-        <dd>Compute transmission terms dynamically</dd>
-      </dl><dl><dt>
-          
-          <code><a href="Exposure.html">Exposure()</a></code> 
-        </dt>
-        <dd>A model for exposure. The function <code>F_b</code> must be define</dd>
+        <dd>Compute the mixing matrix and transmission terms</dd>
       </dl><dl><dt>
           
           <code><a href="LocalFrac.html">LocalFrac()</a></code> 
@@ -264,8 +259,8 @@ <h3 id="availability-of-humans-hosts">Availability of humans / hosts<a class="an
         </dt>
         <dd>Compute availability blood hosts of the i^th species</dd>
       </dl></div><div class="section level2">
+      <h2 id="exposure">Exposure<a class="anchor" aria-label="anchor" href="#exposure"></a></h2>
       
-      <h3 id="exposure">Exposure<a class="anchor" aria-label="anchor" href="#exposure"></a></h3>
       <p class="section-desc"></p><p>Methods to model the force of infection</p>
 
       
@@ -276,9 +271,14 @@ <h3 id="exposure">Exposure<a class="anchor" aria-label="anchor" href="#exposure"
 
       <dl><dt>
           
+          <code><a href="Exposure.html">Exposure()</a></code> 
+        </dt>
+        <dd>Exposure and Infection</dd>
+      </dl><dl><dt>
+          
           <code><a href="F_foi.html">F_foi()</a></code> 
         </dt>
-        <dd>A model for exposure</dd>
+        <dd>A model for daily FoI as a function of the daily EIR.</dd>
       </dl></div><div class="section level2">
       
       <h3 id="poisson-exposure">Poisson Exposure<a class="anchor" aria-label="anchor" href="#poisson-exposure"></a></h3>
@@ -294,7 +294,7 @@ <h3 id="poisson-exposure">Poisson Exposure<a class="anchor" aria-label="anchor"
           
           <code><a href="F_foi.pois.html">F_foi(<i>&lt;pois&gt;</i>)</a></code> 
         </dt>
-        <dd>Null human population births</dd>
+        <dd>A Poisson model for the daily local FoI as a function of the daily EIR.</dd>
       </dl><dl><dt>
           
           <code><a href="setup_exposure_pois.html">setup_exposure_pois()</a></code> 
@@ -315,7 +315,7 @@ <h3 id="negative-binomial-exposure">Negative Binomial Exposure<a class="anchor"
           
           <code><a href="F_foi.nb.html">F_foi(<i>&lt;nb&gt;</i>)</a></code> 
         </dt>
-        <dd>Null human population births</dd>
+        <dd>The daily FoI as a function of the daily EIR under a negative binomial model of exposure.</dd>
       </dl><dl><dt>
           
           <code><a href="setup_exposure_nb.html">setup_exposure_nb()</a></code> 
@@ -3311,6 +3311,31 @@ <h3 id="compute-terms">Compute terms<a class="anchor" aria-label="anchor" href="
           <code><a href="compute_NI_ix.html">compute_NI_ix()</a></code> 
         </dt>
         <dd>Compute NI once</dd>
+      </dl><dl><dt>
+          
+          <code><a href="compute_vars_full.html">compute_vars_full()</a></code> 
+        </dt>
+        <dd>Compute other variables at time t</dd>
+      </dl><dl><dt>
+          
+          <code><a href="compute_vars_human.html">compute_vars_human()</a></code> 
+        </dt>
+        <dd>Compute other variables at time t</dd>
+      </dl><dl><dt>
+          
+          <code><a href="compute_vars_aqua.html">compute_vars_aqua()</a></code> 
+        </dt>
+        <dd>Differential equation models for aquatic mosquito populations</dd>
+      </dl><dl><dt>
+          
+          <code><a href="compute_vars_mosy.html">compute_vars_mosy()</a></code> 
+        </dt>
+        <dd>Compute other variables at time t</dd>
+      </dl><dl><dt>
+          
+          <code><a href="compute_vars_cohort.html">compute_vars_cohort()</a></code> 
+        </dt>
+        <dd>Differential equation models for human cohorts</dd>
       </dl></div><div class="section level2">
       
       <h3 id="plot-terms">Plot terms<a class="anchor" aria-label="anchor" href="#plot-terms"></a></h3>
@@ -3341,7 +3366,7 @@ <h3 id="plot-terms">Plot terms<a class="anchor" aria-label="anchor" href="#plot-
           
           <code><a href="xde_lines_aEIR.html">xde_lines_aEIR()</a></code> 
         </dt>
-        <dd>Add lines for the annualized EIR <em>vs.</em> time</dd>
+        <dd>Add lines for the annualized EIR <em>vs.</em> t</dd>
       </dl><dl><dt>
           
           <code><a href="xde_plot_PR.html">xde_plot_PR()</a></code> 
diff --git a/reference/travel_malaria.html b/reference/travel_malaria.html
index 81dcd257..768aa228 100644
--- a/reference/travel_malaria.html
+++ b/reference/travel_malaria.html
@@ -98,7 +98,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
     
 
-<p>a <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> value</p>
+<p>the travel FoI, a <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> value</p>
     </div>
 
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/xde_lines_EIR.html b/reference/xde_lines_EIR.html
index 0ba33461..9c720f05 100644
--- a/reference/xde_lines_EIR.html
+++ b/reference/xde_lines_EIR.html
@@ -81,17 +81,21 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">xde_lines_EIR</span><span class="op">(</span><span class="va">terms</span>, <span class="va">pars</span>, clrs <span class="op">=</span> <span class="st">"black"</span>, llty <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">xde_lines_EIR</span><span class="op">(</span><span class="va">tm</span>, <span class="va">EIR</span>, <span class="va">nStrata</span>, clrs <span class="op">=</span> <span class="st">"black"</span>, llty <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>terms</dt>
-<dd><p>a list with the outputs of <code><a href="parse_deout.html">exDE::parse_deout()</a></code></p></dd>
+    <dl><dt>tm</dt>
+<dd><p>the time</p></dd>
 
 
-<dt>pars</dt>
-<dd><p>a list that defines an <code>exDE</code> model (<em>e.g.</em>,  generated by <code><a href="xde_setup.html">exDE::xde_setup()</a></code>)</p></dd>
+<dt>EIR</dt>
+<dd><p>the entomological inoculation rate</p></dd>
+
+
+<dt>nStrata</dt>
+<dd><p>the number of human / host population strata</p></dd>
 
 
 <dt>clrs</dt>
diff --git a/reference/xde_lines_PR.html b/reference/xde_lines_PR.html
index 8c1c6943..8c0f6d8d 100644
--- a/reference/xde_lines_PR.html
+++ b/reference/xde_lines_PR.html
@@ -81,17 +81,21 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">xde_lines_PR</span><span class="op">(</span><span class="va">terms</span>, <span class="va">pars</span>, clrs <span class="op">=</span> <span class="st">"black"</span>, llty <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">xde_lines_PR</span><span class="op">(</span><span class="va">tm</span>, <span class="va">PR</span>, <span class="va">nStrata</span>, clrs <span class="op">=</span> <span class="st">"black"</span>, llty <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>terms</dt>
-<dd><p>a list with the outputs of <code><a href="parse_deout.html">exDE::parse_deout()</a></code></p></dd>
+    <dl><dt>tm</dt>
+<dd><p>the time</p></dd>
 
 
-<dt>pars</dt>
-<dd><p>a list that defines an <code>exDE</code> model (<em>e.g.</em>,  generated by <code><a href="xde_setup.html">xde_setup()</a></code>)</p></dd>
+<dt>PR</dt>
+<dd><p>the computed parasite rate</p></dd>
+
+
+<dt>nStrata</dt>
+<dd><p>the number of human / host population strata</p></dd>
 
 
 <dt>clrs</dt>
diff --git a/reference/xde_lines_X_SIS.html b/reference/xde_lines_X_SIS.html
index 229af339..230dc115 100644
--- a/reference/xde_lines_X_SIS.html
+++ b/reference/xde_lines_X_SIS.html
@@ -81,7 +81,7 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">xde_lines_X_SIS</span><span class="op">(</span><span class="va">XH</span>, <span class="va">pars</span>, clrs <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"darkblue"</span>, <span class="st">"darkred"</span><span class="op">)</span>, llty <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">xde_lines_X_SIS</span><span class="op">(</span><span class="va">XH</span>, <span class="va">nStrata</span>, clrs <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"darkblue"</span>, <span class="st">"darkred"</span><span class="op">)</span>, llty <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
@@ -90,8 +90,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 <dd><p>a list with the outputs of parse_deout_X_SIS</p></dd>
 
 
-<dt>pars</dt>
-<dd><p>a list that defines an <code>exDE</code> model (<em>e.g.</em>,  generated by <code><a href="xde_setup.html">xde_setup()</a></code>)</p></dd>
+<dt>nStrata</dt>
+<dd><p>the number of population strata</p></dd>
 
 
 <dt>clrs</dt>
diff --git a/reference/xde_lines_aEIR.html b/reference/xde_lines_aEIR.html
index 8ec1a670..ca8613af 100644
--- a/reference/xde_lines_aEIR.html
+++ b/reference/xde_lines_aEIR.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Add lines for the annualized EIR vs. time"><title>Add lines for the annualized EIR vs. time — xde_lines_aEIR • exDE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Add lines for the annualized EIR vs. time — xde_lines_aEIR"><meta property="og:description" content="Add lines for the annualized EIR vs. time"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Add lines for the annualized EIR vs. t"><title>Add lines for the annualized EIR vs. t — xde_lines_aEIR • exDE</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Add lines for the annualized EIR vs. t — xde_lines_aEIR"><meta property="og:description" content="Add lines for the annualized EIR vs. t"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -70,28 +70,32 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="" class="logo" alt=""><h1>Add lines for the annualized EIR <em>vs.</em> time</h1>
+      <img src="" class="logo" alt=""><h1>Add lines for the annualized EIR <em>vs.</em> t</h1>
       <small class="dont-index">Source: <a href="https://github.com/dd-harp/exDE/blob/HEAD/R/plot-terms.R" class="external-link"><code>R/plot-terms.R</code></a></small>
       <div class="d-none name"><code>xde_lines_aEIR.Rd</code></div>
     </div>
 
     <div class="ref-description section level2">
-    <p>Add lines for the annualized EIR <em>vs.</em> time</p>
+    <p>Add lines for the annualized EIR <em>vs.</em> t</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">xde_lines_aEIR</span><span class="op">(</span><span class="va">terms</span>, <span class="va">pars</span>, clrs <span class="op">=</span> <span class="st">"black"</span>, llty <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">xde_lines_aEIR</span><span class="op">(</span><span class="va">tm</span>, <span class="va">EIR</span>, <span class="va">nStrata</span>, clrs <span class="op">=</span> <span class="st">"black"</span>, llty <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
-    <dl><dt>terms</dt>
-<dd><p>a list with the outputs of <code><a href="parse_deout.html">parse_deout()</a></code></p></dd>
+    <dl><dt>tm</dt>
+<dd><p>the time</p></dd>
 
 
-<dt>pars</dt>
-<dd><p>a list that defines an <code>exDE</code> model (<em>e.g.</em>,  generated by <code><a href="xde_setup.html">exDE::xde_setup()</a></code>)</p></dd>
+<dt>EIR</dt>
+<dd><p>the entomological inoculation rate</p></dd>
+
+
+<dt>nStrata</dt>
+<dd><p>the number of human / host population strata</p></dd>
 
 
 <dt>clrs</dt>
diff --git a/reference/xde_plot_EIR.html b/reference/xde_plot_EIR.html
index 043e6a03..261c80bf 100644
--- a/reference/xde_plot_EIR.html
+++ b/reference/xde_plot_EIR.html
@@ -81,7 +81,14 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">xde_plot_EIR</span><span class="op">(</span><span class="va">pars</span>, clrs <span class="op">=</span> <span class="st">"black"</span>, llty <span class="op">=</span> <span class="fl">1</span>, stable <span class="op">=</span> <span class="cn">FALSE</span>, add_axes <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">xde_plot_EIR</span><span class="op">(</span></span>
+<span>  <span class="va">pars</span>,</span>
+<span>  i <span class="op">=</span> <span class="fl">1</span>,</span>
+<span>  clrs <span class="op">=</span> <span class="st">"black"</span>,</span>
+<span>  llty <span class="op">=</span> <span class="fl">1</span>,</span>
+<span>  stable <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  add_axes <span class="op">=</span> <span class="cn">TRUE</span></span>
+<span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
@@ -90,6 +97,10 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 <dd><p>a list that defines an <code>exDE</code> model (<em>e.g.</em>,  generated by <code><a href="xde_setup.html">exDE::xde_setup()</a></code>)</p></dd>
 
 
+<dt>i</dt>
+<dd><p>the host species index</p></dd>
+
+
 <dt>clrs</dt>
 <dd><p>a vector of colors</p></dd>
 
diff --git a/reference/xde_plot_PR.html b/reference/xde_plot_PR.html
index ac9845be..7f857261 100644
--- a/reference/xde_plot_PR.html
+++ b/reference/xde_plot_PR.html
@@ -81,7 +81,14 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">xde_plot_PR</span><span class="op">(</span><span class="va">pars</span>, clrs <span class="op">=</span> <span class="st">"black"</span>, llty <span class="op">=</span> <span class="fl">1</span>, stable <span class="op">=</span> <span class="cn">FALSE</span>, add_axes <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">xde_plot_PR</span><span class="op">(</span></span>
+<span>  <span class="va">pars</span>,</span>
+<span>  i <span class="op">=</span> <span class="fl">1</span>,</span>
+<span>  clrs <span class="op">=</span> <span class="st">"black"</span>,</span>
+<span>  llty <span class="op">=</span> <span class="fl">1</span>,</span>
+<span>  stable <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  add_axes <span class="op">=</span> <span class="cn">TRUE</span></span>
+<span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
@@ -90,6 +97,10 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 <dd><p>a list that defines an <code>exDE</code> model (<em>e.g.</em>,  generated by <code><a href="xde_setup.html">xde_setup()</a></code>)</p></dd>
 
 
+<dt>i</dt>
+<dd><p>the host species index</p></dd>
+
+
 <dt>clrs</dt>
 <dd><p>a vector of colors</p></dd>
 
diff --git a/reference/xde_plot_aEIR.html b/reference/xde_plot_aEIR.html
index 9fe452ed..a8fa55a1 100644
--- a/reference/xde_plot_aEIR.html
+++ b/reference/xde_plot_aEIR.html
@@ -81,7 +81,14 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">xde_plot_aEIR</span><span class="op">(</span><span class="va">pars</span>, clrs <span class="op">=</span> <span class="st">"black"</span>, llty <span class="op">=</span> <span class="fl">1</span>, stable <span class="op">=</span> <span class="cn">FALSE</span>, add_axes <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">xde_plot_aEIR</span><span class="op">(</span></span>
+<span>  <span class="va">pars</span>,</span>
+<span>  i <span class="op">=</span> <span class="fl">1</span>,</span>
+<span>  clrs <span class="op">=</span> <span class="st">"black"</span>,</span>
+<span>  llty <span class="op">=</span> <span class="fl">1</span>,</span>
+<span>  stable <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  add_axes <span class="op">=</span> <span class="cn">TRUE</span></span>
+<span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
@@ -90,6 +97,10 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 <dd><p>a list that defines an <code>exDE</code> model (<em>e.g.</em>,  generated by <code><a href="xde_setup.html">exDE::xde_setup()</a></code>)</p></dd>
 
 
+<dt>i</dt>
+<dd><p>the host species index</p></dd>
+
+
 <dt>clrs</dt>
 <dd><p>a vector of colors</p></dd>
 
diff --git a/search.json b/search.json
index 79dc31a2..1ea90a3d 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://dd-harp.github.io/exDE/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2022 exDE authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"sec1","dir":"Articles","previous_headings":"","what":"Git workflow","title":"Contributing","text":"exDE project hosted GitHub (repository), use Git workflow similar “Gitflow” (albeit without separate release branch, main takes role), described . Git workflow way use repository way invite collaboration organized way protects latest stable version software unintended changes. new Git need reminders, please check excellent documentation Atlassian. recommend reading “Getting Started” learn set repository, followed “Collaborating” learn work branches, pull requests, merging, common Git activities. workflow designed around branches. main, dev, gh-pages branches always exist repository. branches exist long person(s) working need , deleted merged dev. main: branch contains latest version release exDE, updated CRAN version also updated. PRs submitted except core dev team, updated main mean need update package CRAN various housekeeping tasks accompany version update (.e. create archival release update accepted CRAN). dev: branch PRs collaborators made . version code dev always useable (.e. pass automated tests), contain latest cutting edge features. Periodically dev accumulated sufficient number new features, member core dev team make PR dev main. main updated update CRAN package, often, CRAN request package maintainers submit updates “every 1–2 months”. gh-pages: branch exists support GitHub pages website (one browsing right now). updated automatically pkgdown continuous integration workflow rebuilds website main pushed (.e. PR merged main). gh-pages considered “read-” branch, even core dev team. feat/*: branches starting feat/ collaborators (core dev) names branches updating including new features, including limited code, documentation, tests. example, branch improved documentation document called feat/UpdateContributing. PR feat/ branch merged dev, feat/ branch deleted. PRs never made feat/ branches main. bugfix/*: small bugfixes (spelling errors, misnamed variables, etc), may appropriate make bugfix/ branch. rules apply feat/ branches. branches use GitHub’s branch protection rules enforce rules. Core dev team members can access going Settings -> Branches. main dev protected deletion. PRs made dev must reviewed approved least 1 reviewer allowed merged.  show example workflow . main branch, blue, starts left side, dev created , purple. , two feat/* bugfix/* branches created dev time, shown green. upper one two updates merged back dev, via pull request. pull request, lower one must pull updates dev working latest version code. another update, ready merged dev via pull request. point, decide two features enough version update, make pull request dev main update version 0.1. merged, can start making feat/* bugfix/* branches dev start developing version 0.2!","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"example","dir":"Articles","previous_headings":"Git workflow","what":"Example","title":"Contributing","text":"Let’s say great idea new feature, change improve document. ’s get started Git workflow get feature road merged exDE software. Please note, assume familiarity Git commands . reference meaning commands, please see Git documentation. start work exDE, first clone repository. terminal window, navigate directory want exDE folder appear , run git clone git@github.com:dd-harp/exDE.git, use SSH keys, git clone https://github.com/dd-harp/exDE.git clone HTTPS. links can found click green “Code” button main repository page. clone repository, go inside cd exDE. run git fetch --retrieves information branches remote (repository GitHub website) local repository (one computer). Now switch dev branch git checkout dev. can make sure ’s date running git pull origin dev. Let’s say want call new feature branch feat/UpdateContributing. can make switch running git checkout -b feat/UpdateContributing. push new branch remote repository, run git push origin feat/UpdateContributing. now appear list branches. Now, make changes! recommend editing package RStudio using R project file exDE.Rproj repository. explained Section 3. ready push changes, use git add either add files commit one one, know want add new /modified files, can use git add .. Run git commit -m \"message explaining changes \" make commit message. mind many small commits, Git style, please feel pressure make large commits. Now git push origin feat/UpdateContributing push commit remote branch feat/UpdateContributing! navigate branch GitHub repository, see changes. Now repeat steps 6 9 ready start testing changes submit pull request (covered Sections 4 5).","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"sec2","dir":"Articles","previous_headings":"","what":"The exDE R package","title":"Contributing","text":"exDE R package, going making substantial changes, necessary sense organized package must rebuilt creating documentation, exporting functions, testing. extensive documentation R package structured comes official R manual, Writing R Extensions. shorter guide tips current best practice book R Packages, unfamiliar R packages, reccomend briefly skimming book starting point. building exDE supported pkgdown, responsible automatically building documentation website browsing right now, testthat used test package. files top level directory important aware : _pkgdown.yml: controls website generated, explained article. add delete functions objects documentation package, add delete vignettes, must modify file website build properly. DESCRIPTION: file provides critical information package, documentation official manual R packages book. updated version releases, include additional authors, add additional packages Imports Suggests. NAMESPACE: read-file produced running roxygen2 build documentation package, tells R functions exported package user’s R session load exDE library(exDE). never modified hand. NEWS.md: NEWS page package’s CRAN page well News tab GitHub pages website built file; modified dev team ready update main new version. information, see utils::news help file. README.md: main readme file displayed GitHub repository, main page GitHub pages website, README page package’s CRAN page. rest package organized directories. detail, recommend reading guides linked earlier. .github/: files control GitHub Actions used automatically test package PR made, automatically build package website, automatically check code coverage (% code checked tests). Much detail given Section 6. docs/: contains pkgdown website built pushed gh-pages automatically GitHub Action. trigger manual (local) build website test something using pkgdown::build_site, build folder. folder considered read-. inst/: folder serves many purposes general R packages (see resources details), currently contains CITATION file used generate citation found utils::citation. man/: folder contains package function/object documentation automatically generated roxygen2, considered read-. R/: source code package lives ; describe naming convention files can quickly identify existing code , organize name new code. tests/: within folder sub-directory testthat/ contains automated tests included package. test models initialized equilibrium remain equilibrium integrated time. vignettes/: folder contains .Rmd files contains vignettes R package, longer form articles document specific functionality exDE. available GitHub pages website via top drop menus package’s CRAN page.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"r-folder","dir":"Articles","previous_headings":"The exDE R package","what":"R/ folder","title":"Contributing","text":"model component “base” file ending -interface defines generic interface model component must implement. example human-interface.R defines generic methods human disease model must implement human-SIS.R defines specific methods SIS model human disease dynamics. adult-GeRM.R: generalized Ross-Macdonald model adult mosquito dynamics. aquatic-basic.R: basic competition model aquatic mosquito dynamics. aquatic-trace.R: trace (exogenously forced) model aquatic mosquito dynamics. human-SIS.R: SIS model human disease dynamics. human-SIP.R: SIP model human disease dynamics. human-hMoI.R: hybrid MoI model human disease dynamics. exogenous-null: null () exogenous forcing. vc-null.R: null () vector control. vc-lemenach.R: Le Menach model ITN based adult vector control. diffeqn.R: exDE generalized differential equations implement framework; typically modified. metrics.R: spatial metrics (defined Spatial Dynamics paper) utils.R: utility functions","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"sec3","dir":"Articles","previous_headings":"","what":"Making large changes or additions to exDE","title":"Contributing","text":"reading Section 2 reasonable grasp exDE R package organized, really understand implement new models, detail necessary files one actually modify add. also describe best practices contributors add package making large change. Let’s say someone wanted add new human disease model, say SIR model. basic steps : Within R/, make new file human-SIR.R implement generic methods human-interface.R new model. Also make function named something like make_parameters_human_SIR modify parameter environment implement SIR model. can check human disease models reference. RStudio, run Build -> Document (control/command + shift + D) run roxygen2 builds functions documentation updates NAMESPACE new functions. run Build -> Install Package (control/command + shift + B) re-install load package. works opened exDE.Rproj file RStudio project. Make new vignette named something like “human_vignette.Rmd” vignettes/ describing model parameters, perhaps simple simulation . Make test named something like test-human-sir.R tests/testthat/ tests SIR model behaves expected conditions outcome known (e.g. infected persons present, number susceptible persons can never decrease). Please see testthat documentation R packages chapter testing information. added new functions vignettes, add _pkgdown.yml file appropriate place. can use pkgdown::build_site point test website still builds. go details test package locally Section 4 make pull request Section 5. writing new model modifying existing one, please note exDE achieves modularity extensive use S3 dispatch, similar single dispatch programming languages. details base::UseMethod S3 chapter Advanced R. Use S3 dispatch appears extensively source code exDE. writing new functions, must documented. , existing code provides good reference. exDE depends upon roxygen2 build documentation, website provides help write appropriate tags (e.g. #' @export makes function appear exDE NAMESPACE).","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"sec4","dir":"Articles","previous_headings":"","what":"How to test locally","title":"Contributing","text":"making changes exDE submitting PR, take time local tests make sure package still works. extremely important make sure implement changes, re-document re-install package. RStudio, Build -> Document (control/command + shift + D) re-documents package Build -> Install Package (control/command + shift + B) re-installs package. Without package NAMESPACE file may include changes, library(exDE) using recent version code.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"testthat","dir":"Articles","previous_headings":"How to test locally","what":"testthat","title":"Contributing","text":"added tests, changed existing code want make sure tests still pass, run testthat::test_local run tests. error warning appears, re-run tests make sure false positive (due numerical precision errors, small fraction tests give false positive results). error comes consistently, please fix offending code continuing onward. Remember, tests run tests/testthat can check code specifically put tested! large changes tests cover functionality cases expected behavior known advance. unsure make appropriate tests, please either consult existing test files, make PR without tests tell reviewer yet included tests need help making .","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"devtools","dir":"Articles","previous_headings":"How to test locally","what":"devtools","title":"Contributing","text":"crucial function use devtools::check; includes running local tests also extensive set additional checks R CMD check (see official documentation exactly ). also rebuilds vignettes, takes longer just running tests, normally done seldom, one ready submit PR.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"pkgdown","dir":"Articles","previous_headings":"How to test locally","what":"pkgdown","title":"Contributing","text":"always good idea make sure package website still builds making changes. added removed functions, changed function names, added removed vignettes, need updated _pkgdown.yml accordingly. make sure everything works expected, run pkgdown::build_site, build website locally docs/ folder (open automatically browser done). Please address problems builds successfully.","code":""},{"path":[]},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"how-to-make-a-pr","dir":"Articles","previous_headings":"How to make or review a pull request","what":"How to make a PR","title":"Contributing","text":"point, might little tired reading, maybe somewhat anxious actually contributing . good time say making PR can absolutely collaborative process. following previous sections local tests working, think idea new feature work good addition exDE, please consider submitting PR tagging persons dev team can help get past finish line. make pull request, first, navigate branch made changes (.e. feat/* bugfix/* branch). open PR, follow GitHub documentation Atlassian documentation, remember PRs made dev (e.g. dev “base”). making PR, prompted enter description explains PR . Please ensure PR include many disparate modifications, represents self-contained piece work (.e. submit PRs change human mosquito model; please submit two separate PRs ). Please make sure text description contains following elements: PR addresses solves active issue, tag PR (.e. addresses issue 75, type text box #75 GitHub automatically link two; can also just type # GitHub begin automatically link open issues). PR adds new files R/, tests/testthat, vignettes please list write brief description one. apply auto-generated files (.e. anything docs/, man/, NAMESPACE). PR significantly modifies files, please list write brief descriptions changed. apply auto-generated files (.e. anything docs/, man/, NAMESPACE). -progress PR (.e. tests pass), please tag someone team help describe specific problems encountering. Finally, crucial, select someone review PR using “Reviewers” tab upper right hand corner page. PR merged dev passed review least one team member. point review process can start. reviewer may ask additional changes, remember keep making branch working . PR merged dev, please delete old feat/* bugfix/* branch.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"how-to-review-a-pr","dir":"Articles","previous_headings":"How to make or review a pull request","what":"How to review a PR","title":"Contributing","text":"requested reviewer, ’s responsibility : Evaluate whether proposed addition within scope software (e.g. directly-transmitted diseases outside scope exDE). Ensure PR made dev . code passing tests, identify problems suggest solutions author (see Section 6 details ). PR makes significant modifications exDE, work author (already done ) PR tests vignettes document new functions, added _pkgdown.yml file new features appear website. general, exDE’s design philosophy elegant clear design mirrors mathematical description model preferred fast code cases decision made, please correct obvious inefficiencies (e.g. aware matrix operations try structure parentheses minimize computational cost). confident can provide helpful review addresses (possibly) mathematical, conceptual, design, software issues related PR, please either pass someone else bring additional reviewers. Please either familiar review GitHub docs review PRs. cases may necessary investigate issues locally, branch merged. Assuming branch called feat/MyFeature, : Navigate exDE repository computer git fetch --update information branches present remote git checkout -b feat/MyFeature switch branch git pull origin feat/MyFeature make sure includes recent commits Investigate locally, may push fixes feat/MyFeature sure alert PR author done may expect reviewer make changes branch problems resolved CI tests pass, PR ready merged dev! may want delete merged branch let author know can point.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"sec6","dir":"Articles","previous_headings":"","what":"How to deal with continuous integration","title":"Contributing","text":"exDE use GitHub Actions automatically run continuous integration workflows, automated scripts run triggered certain events (.e. PRs pushing certain branches). 3 workflows run can found .github/workflows: check-standard.yaml: runs R CMD check several common operating systems (see official documentation ). runs time pull request made main dev. pkgdown.yaml: runs pkgdown::build_site_github_pages pushes new website gh-pages branch. runs pushes main (.e. PR merged main) new GitHub release made. test-coverage.yaml: runs covr::codecov updates exDE’s codecov integration. runs pushes main. three workflows standard R packages, originated https://github.com/r-lib/actions. workflows may encounter errors. panic happens. Errors can investigated clicking failing workflow Actions tab, clicking specific failing job(s) left hand side screen “Jobs”. errors displayed. Github Actions documentation also describes diagnose errors. Errors R-CMD-check stemming tests may sometimes due numerical errors; exDE can solve model floating point errors, sometimes false positive errors reported numerical routines encounter problems. Restart tests clicking “Re-run jobs” upper right hand see errors persist. Errors pkgdown likely cause ill-formed _pkgdown.yml file, please consult pkgdown documentation post issue get help. Finally encounter truly strange errors workflows (e.g. software installed, strange operating system specific errors, etc), may .yaml workflow scripts outdated need updated. case find latest updated workflow scripts https://github.com/r-lib/actions/tree/v2-branch/examples. , careful overwrite existing rules execute workflows (.e. update line name onward). can push update branch bugfix/check-standard.yaml, update workflow, example.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"sec7","dir":"Articles","previous_headings":"","what":"How to get ready for a version update","title":"Contributing","text":"(dev team ) sufficient number new features added dev version number exDE increased, sufficient duration time passed since last update CRAN (“every 1–2 months”), time make PR dev main get ready update software. please make sure: open PRs (please resolve close updating version) feat/* bugfix/* branches deleted resolving open PRs update NEWS.md new version number significant additions (consider making links NEWS.md PRs included update) update DESCRIPTION new version number make sure website still builds (test devtools::build_site) please use rhub builder service check package builds without errors Windows using CRAN standards (can use function rhub::check_for_cran ) now ready create PR dev main. following standard procedure (Section 5) exception deleting dev (protected deletion), ready update CRAN version exDE. : make update file cran-comments.md informing CRAN version update, tests pass, etc; follow guide R packages book. use devtools::release actually submit package CRAN, function asks many useful questions make sure package actually ready submitted. new version accepted CRAN make new GitHub release accompany new version. celebrate, go rest.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"sec8","dir":"Articles","previous_headings":"","what":"How to report bugs or raise issues?","title":"Contributing","text":"expect common way users interact GitHub issues tab. first point contact exDE team, please hesitate raise issues may either bug reports, questions, comments/suggestions. prefer rather less communication. considering large feature changes, may nice discuss dev team issue first making feat/* branch submitting PR; also great time solicit collaboration feature development! find bug, please remember include minimum reproducible example bug R code addition describing wrong. Please remember include: exDE version Operating System R version Steps recreate Expected behavior Actual behavior Minimum reproducible example (R code)","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Understanding exDE","text":"goal developing exDE lower costs developing models (e.g. time spent formulating, coding, verifying, debugging, & etc.) realistic enough support decisions affecting malaria policies. operating assumption developing framework software robust decision support malaria policies put demands model-building differ expected scientific publication. models work policy setting, must realistic enough relevant policy discussions. ways, need realism associated computational complexity drove development several comprehensive individual-based models (IBMs), OpenMalaria, eMod, MalariaTools. models developed systems differential equations can replicate advantages come individual-based, wanted software handle computational complexity just well IBMs. advantage using systems differential equations resulting models much easier analyze. wanted framework scale complexity, start simple model, progressively modifying models add realism including: realistic human demography, including age structure, births & deaths, migration. multiple host vector species types spatial heterogeneity spatial dynamics, including human mobility mosquito dispersal realistic mosquito ecology exogenous forcing weather factors time, wanted flexibility isolate analyze various components model. Since framework modular, possible pass inputs one () dynamical components trace function, rather fully coupled model. trivial models also provide way rigorously pressure testing software. think model defining skill set, output variables naturally represent subset possible features, framework make easy build models right subset features. models – Einstein suggested – simple possible, simpler. people agree Einstein principle, provided usable advice . know model right level complexity? One way develop least one model clearly complex provide rigorous model selection suite models varying levels complexity. support decisions affecting malaria policy, model building must nimble. malaria programs integrate sophisticated analytics decision-making, conversation room can shift. time, programmatic priorities needs can change. keep , model builders capability building new models address new concerns. might possible real time, possible new model developed preliminary results within week . goals mind, developed mathematical framework make computation dynamical systems modular. mathematical basis modularity described Spatial Dynamics Malaria Transmission. also developed vignette describes modular forms use describe models implemented exDE.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"structural-elements","dir":"Articles","previous_headings":"","what":"Structural Elements","title":"Understanding exDE","text":"model several parameters describe structure model: nVectors – number distinct mosquito vector species model nHosts – number distinct vertebrate host species model HPop – population density population strata vertebrate host species. length HPop used set value nStrata nPatches – number distinct patches model. nHabitats – number distinct aquatic habitats model. Additional information needed configure model egg laying (see ): membership vector required: \\(^{th}\\) element membership matrix identifies patch belongs. searchQ vector required: \\(^{th}\\) element gives habitat search weight compute egg laying. MYZname – string, corresponding model exDE library, specifies model family adult mosquitoes Lname – string, corresponding model exDE library, specifies model family aquatic mosquito population dynamics used Xname – string, corresponding model exDE library, specifies model family human infection dynamics used","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"dynamical-components","dir":"Articles","previous_headings":"","what":"Dynamical Components","title":"Understanding exDE","text":"developing mathematical framework, identified three inseparable chunks model need internally coherent represented several different ways. chunks represented five distinct processes: Models human ecology parasite / pathogen infection dynamics appear one dynamical component. part computes dynamics infection immunity called \\(\\cal X\\), part describes human demography called \\(\\cal H.\\) two components can’t separated easy way, call chunk \\(\\cal XH\\). derivatives model class \\(\\cal X\\) type computed S3 function dXdt(t, y, pars) parameters model object called Xpar dXdt dispatches class(Xpar) Since multiple host species, Xpar \\(^{th}\\) species pars$Xpar[[]]. demographic model, \\(\\cal H\\), can configured part \\(\\cal X\\) Models adult mosquito ecology parasite / pathogen infection dynamics appear second dynamical component. part computes dynamics infection called \\(\\cal YZ\\), part computes mosquito population dynamics called \\(\\cal M\\). two components can’t separated easy way, call chunk \\(\\cal MYZ\\). derivatives model type computed S3 function dMYZdt(t, y, pars) dMdt(t, y, pars) parameters model object called MYZpar dMYZdt dispatches class(MYZpar) Since multiple host species, MYZpar \\(^{th}\\) species pars$MYZpar[[]]. Models aquatic mosquito ecology called \\(\\cal L\\). derivatives model type computed S3 function dLdt(t, y, pars) dMdt(t, y, pars) parameters model object called Lpar dLdt dispatches class(Lpar) Since multiple host species, Lpar \\(^{th}\\) species pars$Lpar[[]].","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"interfaces","dir":"Articles","previous_headings":"","what":"Interfaces","title":"Understanding exDE","text":"developing modular framework, recognized need develop rigorous yet flexible interface allow different dynamical components interact. connect two dynamical components, developed two well-defined interfaces: blood feeding egg laying.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"blood-feeding","dir":"Articles","previous_headings":"Interfaces","what":"Blood Feeding","title":"Understanding exDE","text":"model blood feeding parasite / pathogen transmission mosquitoes. model constrain mosquito blood feeding rates human fraction sensible ways. possible set values mosquito bionomic parameters static values constrained. Spatial Dynamics Malaria Transmission, introduce fully defined blood feeding module constrains blood feeding rate human fraction using concept resource availability. nPatches\\(>1\\) nStrata\\(>1\\), necessary supply additional information configure mixing matrix, \\(\\beta\\), attached pars$beta[[]][[s]] \\(^{th}\\) host \\(s^{th}\\) vector species. time spent matrix must configured host species vector blood feeding search weights must provided stratum, species. \\(^{th}\\) element \\(s^{th}\\) vector used compute availability hosts blood feeding. circadian weighting function required vector species, used transform \\(^{th}\\) time spent matrix set nVectors matrices describing time risk. demographic matrix must configured mosquito species describes mosquito survival dispersal patches.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"egg-laying","dir":"Articles","previous_headings":"Interfaces","what":"Egg Laying","title":"Understanding exDE","text":"description locations aquatic habitats model egg laying emergence. membership vector must provided: \\(^{th}\\) element index patch habitat found search vector must provided: \\(^{th}\\) element index patch habitat found","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"human-demography","dir":"Articles","previous_headings":"Interfaces","what":"Human Demography","title":"Understanding exDE","text":"exDE provides built-support human demography: births handled object deaths, migration, aging handled configuration dHdt object.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"exogenous-forcing","dir":"Articles","previous_headings":"","what":"Exogenous Forcing","title":"Understanding exDE","text":"software designed handle exogenous forcing weather variables.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"setup-solving","dir":"Articles","previous_headings":"","what":"Setup & Solving","title":"Understanding exDE","text":"set functions developed basic setup related vignette, Ross-Maconald model presented modular form","code":""},{"path":[]},{"path":"https://dd-harp.github.io/exDE/articles/adult_GeRM.html","id":"delay-differential-equations","dir":"Articles","previous_headings":"Differential Equations","what":"Delay Differential Equations","title":"The Generalized Ross-Macdonald Adult Mosquito Model","text":"equations naturally implemented exDE::dMYZdt.RM_dde, can also implemented closely related set odes using exDE::dMYZdt.RM_ode (see ). \\[ \\dot{M} = \\Lambda - \\Omega\\cdot M \\] \\[ \\dot{G} = \\mbox{diag}(f) \\cdot (M-G) - \\nu G -  \\Omega \\cdot G \\] \\[ \\dot{Y} = \\mbox{diag}(fq\\kappa) \\cdot (M-Y) - \\Omega \\cdot Y \\] \\[ \\dot{Z} = e^{-\\Omega \\tau} \\cdot \\mbox{diag}(fq\\kappa_{t-\\tau}) \\cdot (M_{t-\\tau}-Y_{t-\\tau}) - \\Omega \\cdot Z \\] Recall mosquito demography matrix describing mortality dispersal given : \\[ \\Omega =  \\mbox{diag(g)} + \\left(- {\\cal K}\\right) \\cdot \\mbox{diag}(\\sigma) \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_GeRM.html","id":"ordinary-differential-equations","dir":"Articles","previous_headings":"Differential Equations","what":"Ordinary Differential Equations","title":"The Generalized Ross-Macdonald Adult Mosquito Model","text":"following, equation solved exDE::dMYZdt.RM_ode. system ODEs except equation giving rate change infectious mosquito density, becomes: \\[ \\dot{Z} = e^{-\\Omega \\tau} \\cdot \\mbox{diag}(fq\\kappa) \\cdot (M-Y) - \\Omega \\cdot Z \\] resulting set equations similar spirit simple model presented Smith & McKenzie (2004) mortality dispersal EIP accounted , time lag . transient dynamics ODE model equal DDE model, equilibrium values, numerical work requiring finding equilibrium points, faster ODE model can safely substituted.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_GeRM.html","id":"equilibrium-solutions","dir":"Articles","previous_headings":"","what":"Equilibrium solutions","title":"The Generalized Ross-Macdonald Adult Mosquito Model","text":"two logical ways begin solving non-trivial equilibrium. first assumes \\(\\Lambda\\) known, implies good knowledge mosquito ecology. second assumes \\(Z\\) known, implies knowledge biting rate human population. show .","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_GeRM.html","id":"starting-with-lambda","dir":"Articles","previous_headings":"Equilibrium solutions","what":"Starting with \\(\\Lambda\\)","title":"The Generalized Ross-Macdonald Adult Mosquito Model","text":"Piven \\(\\Lambda\\) can solve: \\[ M = \\Omega^{-1} \\cdot \\Lambda \\] given \\(M\\) set \\(\\dot{Y}\\) zero factor \\(Y\\) get: \\[ Y = (\\mbox{diag}(fq\\kappa) + \\Omega)^{-1} \\cdot \\mbox{diag}(fq\\kappa) \\cdot M \\] set \\(\\dot{Z}\\) zero get: \\[ Z = \\Omega^{-1} \\cdot e^{-\\Omega \\tau} \\cdot \\mbox{diag}(fq\\kappa) \\cdot (M-Y) \\] dynamics \\(P\\) independent infection dynamics, can solve given \\(M\\) : \\[ G = (\\Omega + \\mbox{diag}(f+\\nu))^{-1} \\cdot \\mbox{diag}(f) \\cdot M \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_GeRM.html","id":"starting-with-z","dir":"Articles","previous_headings":"Equilibrium solutions","what":"Starting with \\(Z\\)","title":"The Generalized Ross-Macdonald Adult Mosquito Model","text":"common start estimate \\(Z\\), perhaps derived estimated EIR (entomological inoculation rate). Piven \\(Z\\), can calculate state variables \\(\\Lambda\\). numerical implementation, note \\((e^{-\\Omega\\tau})^{-1} = e^{\\Omega\\tau}\\). \\[ M-Y = \\mbox{diag}(1/fq\\kappa) \\cdot (e^{-\\Omega\\tau})^{-1} \\cdot \\Omega \\cdot Z \\] \\[ Y = \\Omega^{-1} \\cdot \\mbox{diag}(fq\\kappa) \\cdot (M-Y) \\] \\[ M = (M - Y) + Y \\] \\[ \\Lambda = \\Omega \\cdot M \\] can use equation \\(G\\) .","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_GeRM.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"The Generalized Ross-Macdonald Adult Mosquito Model","text":"show example starting solving model equilibrium. Please note runs adult mosquito model users read fully worked example run full simulation.","code":"library(exDE) library(expm) library(deSolve) library(data.table) library(ggplot2) nPatches <- 3 params <- make_parameters_xde(\"ode\") params$nPatches <- nPatches params$nVectors =1"},{"path":"https://dd-harp.github.io/exDE/articles/adult_GeRM.html","id":"the-ross-macdonald-parameterization","dir":"Articles","previous_headings":"Example","what":"The Ross-Macdonald Parameterization","title":"The Generalized Ross-Macdonald Adult Mosquito Model","text":"RM model, can set parameters simulation 3 patches. Now set values \\(\\kappa\\) \\(\\Lambda\\) solve equilibrium values. use exDE::make_inits_MYZ_RM store initial values. equations implemented compute \\(\\Upsilon\\) dynamically, attach Upsilon initial values: set indices exDE::make_indices. can set initial conditions vector use deSolve::ode solve model. Normally values computed within exDE::xDE_diffeqn. , set local version: output plotted . flat lines shown verification steady state solutions computed match steady states computed solving equations:","code":"f <- 0.3 q <- 0.9 g <- 1/20 sigma <- 1/10 eip <- 11 nu <- 1/2 eggsPerBatch <- 30  calK <- matrix(0, nPatches, nPatches) calK[1, 2:3] <- c(0.2, 0.8) calK[2, c(1,3)] <- c(0.5, 0.5) calK[3, 1:2] <- c(0.7, 0.3) calK <- t(calK)  Omega <- make_Omega(g, sigma, calK, nPatches) Upsilon <- expm::expm(-Omega * eip)  params = make_parameters_MYZ_GeRM(params, g, sigma, f, q, nu, eggsPerBatch, eip, calK, solve_as = \"ode\") kappa <- c(0.1, 0.075, 0.025) Lambda <- c(5, 10, 8)  Omega_inv <- solve(Omega)  M_eq <- as.vector(Omega_inv %*% Lambda) G_eq <- as.vector(solve(diag(f+nu, nPatches) + Omega) %*% diag(f, nPatches) %*% M_eq) Y_eq <- as.vector(solve(diag(f*q*kappa) + Omega) %*% diag(f*q*kappa) %*% M_eq) Z_eq <- as.vector(Omega_inv %*% Upsilon %*% diag(f*q*kappa) %*% (M_eq - Y_eq)) params = make_inits_MYZ_GeRM_ode(pars = params,                               M0 = M_eq, G0 = G_eq, Y0 = Y_eq, Z0 = Z_eq) params$Lambda[[1]] = Lambda  params$kappa[[1]] = kappa params = make_indices(params) y0 = get_inits_MYZ(params, 1)    dMYZdt_local = function(t, y, pars, s=1) {   list(dMYZdt(t, y, pars, s)) }  out <- deSolve::ode(y = y0, times = 0:50, dMYZdt_local, parms=params,                      method = 'lsoda', s=1) colnames(out)[params$ix$MYZ[[1]]$M_ix+1] <- paste0('M_', 1:params$nPatches) colnames(out)[params$ix$MYZ[[1]]$G_ix+1] <- paste0('G_', 1:params$nPatches) colnames(out)[params$ix$MYZ[[1]]$Y_ix+1] <- paste0('Y_', 1:params$nPatches) colnames(out)[params$ix$MYZ[[1]]$Z_ix+1] <- paste0('Z_', 1:params$nPatches)  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Patch\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Patch)) +   geom_line() +   facet_wrap(. ~ Component, scales = 'free') +   theme_bw()"},{"path":[]},{"path":"https://dd-harp.github.io/exDE/articles/adult_RM.html","id":"delay-differential-equations","dir":"Articles","previous_headings":"Differential Equations","what":"Delay Differential Equations","title":"A Ross-Macdonald Adult Mosquito Model","text":"equations naturally implemented exDE::dMYZdt.RM_dde, can also implemented closely related set odes using exDE::dMYZdt.RM_ode (see ). \\[ \\dot{M} = \\Lambda - \\Omega\\cdot M \\] \\[ \\dot{P} = \\mbox{diag}(f) \\cdot (M-P) -  \\Omega \\cdot P \\] \\[ \\dot{Y} = \\mbox{diag}(fq\\kappa) \\cdot (M-Y) - \\Omega \\cdot Y \\] \\[ \\dot{Z} = e^{-\\Omega \\tau} \\cdot \\mbox{diag}(fq\\kappa_{t-\\tau}) \\cdot (M_{t-\\tau}-Y_{t-\\tau}) - \\Omega \\cdot Z \\] Recall mosquito demography matrix describing mortality dispersal given : \\[ \\Omega =  \\mbox{diag(g)} + \\left(- {\\cal K}\\right) \\cdot \\mbox{diag}(\\sigma) \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_RM.html","id":"ordinary-differential-equations","dir":"Articles","previous_headings":"Differential Equations","what":"Ordinary Differential Equations","title":"A Ross-Macdonald Adult Mosquito Model","text":"following, equation solved exDE::dMYZdt.RM_ode. system ODEs except equation giving rate change infectious mosquito density, becomes: \\[ \\dot{Z} = e^{-\\Omega \\tau} \\cdot \\mbox{diag}(fq\\kappa) \\cdot (M-Y) - \\Omega \\cdot Z \\] resulting set equations similar spirit simple model presented Smith & McKenzie (2004)2. mortality dispersal EIP accounted , time lag . transient dynamics ODE model equal DDE model, equilibrium values, numerical work requiring finding equilibrium points, faster ODE model can safely substituted.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_RM.html","id":"equilibrium-solutions","dir":"Articles","previous_headings":"","what":"Equilibrium solutions","title":"A Ross-Macdonald Adult Mosquito Model","text":"two logical ways begin solving non-trivial equilibrium. first assumes \\(\\Lambda\\) known, implies good knowledge mosquito ecology. second assumes \\(Z\\) known, implies knowledge biting rate human population. show .","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_RM.html","id":"starting-with-lambda","dir":"Articles","previous_headings":"Equilibrium solutions","what":"Starting with \\(\\Lambda\\)","title":"A Ross-Macdonald Adult Mosquito Model","text":"Piven \\(\\Lambda\\) can solve: \\[ M = \\Omega^{-1} \\cdot \\Lambda \\] given \\(M\\) set \\(\\dot{Y}\\) zero factor \\(Y\\) get: \\[ Y = (\\mbox{diag}(fq\\kappa) + \\Omega)^{-1} \\cdot \\mbox{diag}(fq\\kappa) \\cdot M \\] set \\(\\dot{Z}\\) zero get: \\[ Z = \\Omega^{-1} \\cdot e^{-\\Omega \\tau} \\cdot \\mbox{diag}(fq\\kappa) \\cdot (M-Y) \\] dynamics \\(P\\) independent infection dynamics, can solve given \\(M\\) : \\[ P = (\\Omega + \\mbox{diag}(f))^{-1} \\cdot \\mbox{diag}(f) \\cdot M \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_RM.html","id":"starting-with-z","dir":"Articles","previous_headings":"Equilibrium solutions","what":"Starting with \\(Z\\)","title":"A Ross-Macdonald Adult Mosquito Model","text":"common start estimate \\(Z\\), perhaps derived estimated EIR (entomological inoculation rate). Piven \\(Z\\), can calculate state variables \\(\\Lambda\\). numerical implementation, note \\((e^{-\\Omega\\tau})^{-1} = e^{\\Omega\\tau}\\). \\[ M-Y = \\mbox{diag}(1/fq\\kappa) \\cdot (e^{-\\Omega\\tau})^{-1} \\cdot \\Omega \\cdot Z \\] \\[ Y = \\Omega^{-1} \\cdot \\mbox{diag}(fq\\kappa) \\cdot (M-Y) \\] \\[ M = (M - Y) + Y \\] \\[ \\Lambda = \\Omega \\cdot M \\] can use equation \\(P\\) .","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_RM.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"A Ross-Macdonald Adult Mosquito Model","text":"show example starting solving model equilibrium. Please note runs adult mosquito model users read fully worked example run full simulation.","code":"library(exDE) library(expm) library(deSolve) library(data.table) library(ggplot2)"},{"path":"https://dd-harp.github.io/exDE/articles/adult_RM.html","id":"the-long-way","dir":"Articles","previous_headings":"Example","what":"The long way","title":"A Ross-Macdonald Adult Mosquito Model","text":"set parameters simulation 3 patches. Now set parameter environment correct class using exDE::make_parameters_MYZ_RM, noting solving ode. Now set values \\(\\kappa\\) \\(\\Lambda\\) solve equilibrium values. use exDE::make_inits_MYZ_RM store initial values. equations implemented compute \\(\\Upsilon\\) dynamically, attach Upsilon initial values: set indices exDE::make_indices. can set initial conditions vector use deSolve::ode solve model. Normally values computed within exDE::xDE_diffeqn. , set local version: output plotted . flat lines shown verification steady state solutions computed match steady states computed solving equations:","code":"nPatches <- 3 f <- 0.3 q <- 0.9 g <- 1/20 sigma <- 1/10 eip <- 11 nu <- 1/2 eggsPerBatch <- 30  calK <- matrix(0, nPatches, nPatches) calK[1, 2:3] <- c(0.2, 0.8) calK[2, c(1,3)] <- c(0.5, 0.5) calK[3, 1:2] <- c(0.7, 0.3) calK <- t(calK)  Omega <- make_Omega(g, sigma, calK, nPatches) Upsilon <- expm::expm(-Omega * eip) params <- list(nPatches = nPatches)  params = make_parameters_MYZ_RM(params,                                  g = g, sigma = sigma, calK = calK,                                  f = f, q = q,                                  nu = nu, eggsPerBatch = eggsPerBatch,                                  eip = eip, solve_as = 'ode') kappa <- c(0.1, 0.075, 0.025) Lambda <- c(5, 10, 8)  Omega_inv <- solve(Omega)  M_eq <- as.vector(Omega_inv %*% Lambda) P_eq <- as.vector(solve(diag(f, nPatches) + Omega) %*% diag(f, nPatches) %*% M_eq) Y_eq <- as.vector(solve(diag(f*q*kappa) + Omega) %*% diag(f*q*kappa) %*% M_eq) Z_eq <- as.vector(Omega_inv %*% Upsilon %*% diag(f*q*kappa) %*% (M_eq - Y_eq)) params = make_inits_MYZ_RM_ode(pars = params,                               M0 = M_eq, P0 = P_eq, Y0 = Y_eq, Z0 = Z_eq) params$max_ix = 0  params = make_indices(params) y0 = get_inits_MYZ(params, 1)    dMYZdt_local = func=function(t, y, pars, Lambda, kappa, s) {   pars$Lambda[[s]] = Lambda   pars$kappa[[s]] = kappa    list(dMYZdt(t, y, pars, s)) }  out <- deSolve::ode(y = y0, times = 0:50, dMYZdt_local, parms=params,                      method = 'lsoda', Lambda = Lambda, kappa = kappa, s=1)  out1 <- out colnames(out)[params$MYZpar$M_ix+1] <- paste0('M_', 1:params$nPatches) colnames(out)[params$MYZpar$P_ix+1] <- paste0('P_', 1:params$nPatches) colnames(out)[params$MYZpar$Y_ix+1] <- paste0('Y_', 1:params$nPatches) colnames(out)[params$MYZpar$Z_ix+1] <- paste0('Z_', 1:params$nPatches)  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Patch\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Patch)) +   geom_line() +   facet_wrap(. ~ Component, scales = 'free') +   theme_bw()"},{"path":"https://dd-harp.github.io/exDE/articles/adult_RM.html","id":"setup-utilities","dir":"Articles","previous_headings":"Example","what":"Setup Utilities","title":"A Ross-Macdonald Adult Mosquito Model","text":"vignette , set function solve differential equation. hope helps end user understand exDE works hood, point exDE lower costs building, analyzing, using models. functionality exDE can handle case – can set solve model using built-setup utilities. Learning use utilities makes easy set models without learn internals. set model parameters , make three list named parameters values. also attach list initial values want use, applicable. Ross-Macdonald adult mosquito model, attach parameter values: one dynamical components configurable trace algorithm computes derivatives, passes output parameter (see human-trace.R. configure Xpar, attach values kappa list: Similarly, configure trace algorithm aquatic mosquitoes (see aquatic-trace.R). set model, call xde_setup nPatches set 3 MYZname set “RM” run Ross-Macdonald model adult mosquitoes; pass options, write MYZopts = MYZo; finally, dispersal matrix calK passed calK=calK Xname set “trace” run trace module human infection dynamics Lname set “trace” run trace module aquatic mosquitoes Otherwise, setup takes care internals: Now, can solve equations using xde_solve compare output got . identical, two objects identical, can simply add absolute value differences:","code":"MYZo = list(   f = 0.3, q = 0.9, g = 1/20, sigma = 1/10,   eip = 11, nu = 1/2, eggsPerBatch = 30,   solve_as = \"ode\",    M0 = M_eq, P0 = P_eq, Y0 = Y_eq, Z0 = Z_eq ) Xo = list(kappa =  c(0.1, 0.075, 0.025)) Lo = list(Lambda = c(5, 10, 8)) xde_setup(MYZname = \"RM\", Xname = \"trace\", Lname = \"trace\",       nPatches=3, calK=calK, membership = c(1:3),      residence = c(1:3), HPop = rep(1, 3),     MYZopts = MYZo, Xopts = Xo, Lopts = Lo) -> MYZeg xde_solve(MYZeg, Tmax=50, dt=1) -> MYZeg  out2 <- MYZeg$outputs$orbits$deout sum(abs(out1-out2))==0  #> [1] TRUE"},{"path":"https://dd-harp.github.io/exDE/articles/aqua_basic.html","id":"differential-equations","dir":"Articles","previous_headings":"","what":"Differential Equations","title":"Basic Competition Aquatic Mosquito Model","text":"Given \\(\\Lambda\\) egg laying rate adult mosquito population formulate solve dynamical model aquatic mosquitoes give emergence rate. However, example simply use trace-based (forced) emergence model, \\(\\Lambda\\) completely specifies aquatic mosquitoes. simplest model aquatic (immature) mosquito dynamics negative feedback (density dependence) : \\[ \\dot{L} = \\eta - (\\psi+\\phi+\\theta L)L \\] equations allow number larval habitats \\(l\\) differ \\(p\\), general emergence rate given : \\[ \\Lambda = \\mathcal{N}\\cdot \\alpha \\] \\(\\mathcal{N}\\) \\(p\\times l\\) matrix \\(\\alpha\\) length \\(l\\) column vector given : \\[ \\alpha = \\psi L \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/aqua_basic.html","id":"equilibrium-solutions","dir":"Articles","previous_headings":"","what":"Equilibrium solutions","title":"Basic Competition Aquatic Mosquito Model","text":"general, know value \\(\\Lambda\\) equilibrium can solve \\(L\\) directly using two equations. can consider \\(\\theta\\), strength density dependence unknown solve : \\[ \\theta = (\\eta - \\psi L - \\phi L) / L^2 \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/aqua_basic.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"Basic Competition Aquatic Mosquito Model","text":"","code":"library(exDE) library(deSolve) library(data.table) library(ggplot2)"},{"path":"https://dd-harp.github.io/exDE/articles/aqua_basic.html","id":"the-long-way","dir":"Articles","previous_headings":"Example","what":"The long way","title":"Basic Competition Aquatic Mosquito Model","text":"run simple example 3 aquatic habitats equilibrium. use exDE::make_parameters_L_basic set parameters. Please note runs aquatic mosquito component users read fully worked example run full simulation.","code":"nHabitats <- 3 alpha <- c(10, 50, 20) eta <- c(250, 500, 170) psi <- 1/10 phi <- 1/12 L <- alpha/psi theta <- (eta - psi*L - phi*L)/(L^2) params <- make_parameters_xde()  params$nHabitats = nHabitats params$eggs_laid = list()  params$eggs_laid[[1]] = eta  F_eta = function(t, pars){   pars$eggs_laid[[1]] }  params = make_parameters_L_basic(pars = params, psi = psi, phi = phi, theta = theta) params = make_inits_L_basic(params, L0=L)  params = make_indices(params) xDE_aquatic = function(t, y, pars, F_eta) {   pars$eggs_laid[[1]] <- F_eta(t, pars)   dL <- dLdt(t, y, pars, 1)   return(list(c(dL))) } y0 <- get_inits(params)   out <- deSolve::ode(y = y0, times = 0:50, xDE_aquatic, parms = params, method = 'lsoda', F_eta = F_eta)  out1 <- out colnames(out)[params$L_ix+1] <- paste0('L_', 1:params$nHabitats)  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Patch\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Patch)) +   geom_line() +   theme_bw()"},{"path":"https://dd-harp.github.io/exDE/articles/aqua_basic.html","id":"using-setup","dir":"Articles","previous_headings":"Example","what":"Using Setup","title":"Basic Competition Aquatic Mosquito Model","text":"function xde_setup_aquatic sets model includes aquatic dynamics, solved using xde_solve.aqua. setup functions simpler xde_setup come constrained choices. user can configure aquatic model (trace wouldn’t make much sense), uses Gtrace force egg laying. configure aquatic model: Lo list parameter values attached. use MYZ model Gtrace configure egg laying.","code":"Lo = list(   psi = 1/10,    phi = 1/12 ) alpha = c(10, 50, 20) Lo$L0 = with(Lo, alpha/psi)  Lo$theta = with(Lo, (eta - psi*L0 - phi*L0)/(L0^2)) Mo = list(Gm = c(250, 500, 170)) xde_setup_aquatic(nHabitats = 3, Lname = \"basic\", Lopts = Lo, MYZopts = Mo) -> aqbasic xde_solve(aqbasic, Tmax=50, dt=1)$output$orbits$deout -> out2 sum(abs(out1-out2)) == 0 #> [1] TRUE"},{"path":"https://dd-harp.github.io/exDE/articles/aqua_trace.html","id":"a-forced-model","dir":"Articles","previous_headings":"","what":"A forced model","title":"Trace (exogenously forced) Aquatic Mosquito Model","text":"null model aquatic mosquito dynamics; endogenous dynamics model simply specified Lambda, rate adult mosquitoes spontaneously emerge aquatic habitats. show example, taken package tests, using trace-based aquatic model keep adult mosquito model equilibrium using unequal numbers aquatic habitats per patch.","code":"library(exDE) library(MASS) library(expm) library(deSolve) library(data.table) library(ggplot2)"},{"path":"https://dd-harp.github.io/exDE/articles/aqua_trace.html","id":"the-long-way","dir":"Articles","previous_headings":"A forced model","what":"The Long Way","title":"Trace (exogenously forced) Aquatic Mosquito Model","text":"First, set parameter values. Next, calculate equilibrium values following Ross-Macdonald vignette. use \\(\\mathcal{N}\\) \\(\\mathcal{U}\\) describe aquatic habitats dispersed amongst patches, mosquitoes patch disperse eggs habitat, respectively. Please note unequal numbers aquatic habitats patches, use MASS::ginv compute generalized inverse \\(\\mathcal{N}\\) get \\(\\alpha\\) required equilibrium. Now set model. Please see Ross-Macdonald vignette details adult model. use alpha Lambda parameter forced emergence model, exDE::make_parameters_L_trace. , running full transmission model, must use exDE::MosquitoBehavior pass equilibrium values bionomic parameters exDE::xDE_diffeqn_mosy.","code":"nPatches <- 3 nHabitats <- 4 f <- 0.3 q <- 0.9 g <- 1/20 sigma <- 1/10 eip <- 11 nu <- 1/2 eggsPerBatch <- 30  calN <- matrix(0, nPatches, nHabitats) calN[1,1] <- 1 calN[2,2] <- 1 calN[3,3] <- 1 calN[3,4] <- 1  calU <- matrix(0, nHabitats, nPatches) calU[1,1] <- 1 calU[2,2] <- 1 calU[3:4,3] <- 0.5  calK <- matrix(0, nPatches, nPatches) calK[1, 2:3] <- c(0.2, 0.8) calK[2, c(1,3)] <- c(0.5, 0.5) calK[3, 1:2] <- c(0.7, 0.3) calK <- t(calK)  Omega <- make_Omega(g, sigma, calK, nPatches) Upsilon <- expm::expm(-Omega * eip)  kappa <- c(0.1, 0.075, 0.025) Lambda <- c(5, 10, 8) # equilibrium solutions Omega_inv <- solve(Omega)  M_eq <- as.vector(Omega_inv %*% Lambda) P_eq <- as.vector(solve(diag(f, nPatches) + Omega) %*% diag(f, nPatches) %*% M_eq)  # the \"Lambda\" for the dLdt model alpha <- as.vector(ginv(calN) %*% Lambda) params = make_parameters_xde() class(params$BFpar) <- \"static\" class(params$EGGpar) <- \"simple\" params$nVectors = 1  params$nHosts = 1  params$nPatches = nPatches params$nHabitats = nHabitats params$calU[[1]] = calU params$calN = calN   # ODE params$beta = beta params = make_parameters_L_trace(pars = params, Lambda = alpha) params = make_parameters_MYZ_basicM(pars = params, g = g, sigma = sigma, calK = calK, f = f, q = q, nu = nu, eggsPerBatch = eggsPerBatch) params = make_inits_MYZ_basicM(params, M0=M_eq, P0=P_eq)  params = make_indices(params) y0 <- rep(0, params$max_ix) y0[params$ix$MYZ[[1]]$M_ix] <- M_eq y0[params$ix$MYZ[[1]]$P_ix] <- P_eq  out <- deSolve::ode(y = y0, times = 0:50, func = xDE_diffeqn_mosy, parms = params, method = 'lsoda') out1 <- out colnames(out)[params$ix$MYZ[[1]]$M_ix+1] <- paste0('M_', 1:params$nPatches) colnames(out)[params$ix$MYZ[[1]]$P_ix+1] <- paste0('P_', 1:params$nPatches)  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Patch\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Patch)) +   geom_line() +   facet_wrap(. ~ Component, scales = 'free') +   theme_bw()"},{"path":"https://dd-harp.github.io/exDE/articles/aqua_trace.html","id":"using-setup","dir":"Articles","previous_headings":"A forced model","what":"Using Setup","title":"Trace (exogenously forced) Aquatic Mosquito Model","text":"","code":"Lo = list(   Lambda = alpha  ) MYZo = list(   f = 0.3,   q = 0.9,   g = 1/20,   sigma = 1/10,   eip = 11,   nu = 1/2,   eggsPerBatch = 30,   M0=M_eq,   P0=P_eq ) xde_setup_mosy(MYZname = \"basicM\", Lname = \"trace\",                 nPatches = 3, membership = c(1,2,3,3),                 MYZopts = MYZo, calK = calK, Lopts = Lo,                 kappa = c(0.1, 0.075, 0.025))->mosy1 xde_solve(mosy1,Tmax=50,dt=1)$outputs$orbits$deout -> out2 sum(out2-out1) #> [1] 0"},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"5-3-4 Example","text":"show setup, solve, analyze models mosquito-borne pathogen transmission dynamics control using modular software. vignette designed explain modular notation constructing model five aquatic habitats (\\(l=5\\)), three patches (\\(p=3\\)), four human population strata (\\(n=4\\)). call 5-3-4.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"diagram","dir":"Articles","previous_headings":"Introduction","what":"Diagram","title":"5-3-4 Example","text":"model 5-3-4 designed illustrate important features framework notation. assume : first three habitats found patch 1; last two patch 2; patch 3 habitats. patch 1 residents; patches 2 3 occupied, two different population strata; Transmission among patches modeled using concept time spent, similar visitation rates used models. strata residency (.e; patch spend time ), stratum allocates time across habitats.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"parameters","dir":"Articles","previous_headings":"","what":"Parameters","title":"5-3-4 Example","text":"already know three important parameters, \\(l\\), \\(p\\) \\(n\\) determined early stages model building. exDE package expects parameters contained list object, containing nHabitats, nPatches, nStrata correspond l, p n.","code":"params = make_parameters_xde()  params$nVectors = 1 params$nHosts = 1 params$nHabitats = 5 params$nPatches = 3 params$nStrata = 4"},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"aquatic-habitat-membership-matrix","dir":"Articles","previous_headings":"Parameters","what":"Aquatic Habitat Membership Matrix","title":"5-3-4 Example","text":"aquatic habitat membership matrix \\(\\mathcal{N}\\) \\(p \\times l\\) matrix mapping aquatic habitats patches contain . attached directly parameters list. \\[\\begin{equation} {\\cal N} = \\left[ \\begin{array}{ccccc} 1 & 1 & 1 & 0 & 0 \\\\ 0 & 0 & 0 & 1 & 1\\\\ 0 & 0 & 0 & 0 & 0\\\\ \\end{array} \\right] \\end{equation}\\]","code":"calN <- matrix(  data = c(1,1,1,0,0,       0,0,0,1,1,       0,0,0,0,0),   nrow = params$nPatches, ncol = params$nHabitats, byrow = TRUE ) params$calN <- calN"},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"egg-dispersal-matrix","dir":"Articles","previous_headings":"Parameters","what":"Egg Dispersal Matrix","title":"5-3-4 Example","text":"egg dispersal matrix \\(\\mathcal{U}\\) \\(l \\times p\\) matrix describing eggs laid adult mosquitoes patch allocated among aquatic habitats patch. also attached directly parameters list. \\[\\begin{equation} {\\cal U} = \\left[ \\begin{array}{ccccc} .7 & 0 & 0\\\\ .2 & 0 & 0\\\\ .1 & 0 & 0\\\\ 0 & .8 & 0\\\\ 0 & .2 & 0\\\\ \\end{array} \\right] \\end{equation}\\]","code":"xi <- matrix(c(.7, .2, .1, .8, .2), 5, 1)  params$EGGpar$searchWts[[1]] <- as.vector(xi) params$calU[[1]]<- t(calN %*% diag(as.vector(xi)))"},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"aquatic-mosquito-parameters","dir":"Articles","previous_headings":"Parameters","what":"Aquatic Mosquito Parameters","title":"5-3-4 Example","text":"simulation, use basic competition model larval dynamics (see ). requires specification three parameters, \\(\\psi\\) (maturation rates), \\(\\phi\\) (density-independent mortality rates), \\(\\theta\\) (density-dependent mortality terms), initial conditions. function exDE::make_parameters_L_basic basic checking input parameters returns list correct class method dispatch. returned list attached main parameter list name Lpar.","code":"L0 <- rep(1, params$nHabitats) psi <- rep(1/8, params$nHabitats) phi <- rep(1/8, params$nHabitats) theta <- c(1/10, 1/20, 1/40, 1/100, 1/10)   params = make_parameters_L_basic(params, psi = psi, phi = phi, theta = theta) params = make_inits_L_basic(params, L0=L0)"},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"adult-mosquito-parameters","dir":"Articles","previous_headings":"Parameters","what":"Adult Mosquito Parameters","title":"5-3-4 Example","text":"use ODE version generalized Ross-Macdonald model (see ). Part specification parameters includes construction mosquito dispersal matrix \\(\\mathcal{K}\\), mosquito demography matrix \\(\\Omega\\). Like aquatic parameters, use exDE::make_parameters_MYZ_RM_ode check parameter types return list correct class method dispatch. attach returned list main parameter list name MYZpar.","code":"g <- 1/12 sigma <- 1/12/2 f <- 1/3 q <- 0.9 nu <- c(1/3,1/3,0)   eggsPerBatch <- 30  eip <- 12   calK <- t(matrix(  c(c(0, .6, .3),    c(.4, 0, .7),    c(.6, .4, 0)), 3, 3))  M0 <- rep(100, params$nPatches) P0 <- rep(10, params$nPatches) Y0 <- rep(1, params$nPatches) Z0 <- rep(0, params$nPatches)  Omega <- make_Omega(g, sigma, calK, params$nPatches) Upsilon <- expm::expm(-Omega*eip)  params = make_parameters_MYZ_RM(pars = params, g = g,                  sigma = sigma, calK=calK,                  eip=eip, f=f, q=q, nu=nu,                  eggsPerBatch=eggsPerBatch,                  solve_as = \"ode\")   params = make_inits_MYZ_RM_ode(params, M0=M0, P0=P0,               Y0=Y0, Z0=Z0)"},{"path":[]},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"mixing","dir":"Articles","previous_headings":"Parameters","what":"Mixing","title":"5-3-4 Example","text":"use static demographic model, assumes constant population size (constant \\(H\\)). model, define four population strata. can describe residency vector describing residence: Although directly used example, create residency membership matrix \\(\\mathcal{J}\\), \\(p \\times n\\) matrix indicating patch human population strata resides . \\[\\begin{equation} {\\cal J} = \\left[ \\begin{array}{cccc} 0 & 0 & 0 & 0 \\\\ 1 & 1 & 0 & 0 \\\\ 0 & 0 & 1 & 1 \\\\ \\end{array} \\right] \\end{equation}\\] create time risk matrix \\(\\Psi\\), \\(p \\times n\\) matrix describing human strata spends time across patches. \\[\\begin{equation} \\Psi= \\left[ \\begin{array}{cccc} 0.01 & .01 & .001 & .001 \\\\ 0.95 & .92 & .04 & .02 \\\\ 0.04 & .02 & .959 & .929 \\\\ \\end{array} \\right] \\end{equation}\\] use basic SIS (Susceptible-Infected-Susceptible) model human component (see ). set like rest components, using exDE::make_parameters_X_SIS make correct return type, attached parameter list name Xpar.","code":"H <- matrix(c(10,90, 100, 900), 4, 1) params = setup_Hpar_static(params, 1, HPop=H) residence = c(2,2,3,3) searchWtsH = c(1,1,1,1) params = setup_BloodFeeding(params, 1, 1, residence=residence, searchWts=searchWtsH) calJ <- t(matrix(  c(c(0,0,0,0),   c(1,1,0,0),   c(0,0,1,1)), 4, 3 )) TaR <- t(matrix(  c(c(0.01,0.01,0.001,0.001),   c(.95,.92,.04,.02),   c(.04,.02,.959,.929)), 4, 3 )) params$BFpar$TaR[[1]][[1]] <- TaR I0 <- as.vector(0.2*H) r <- 1/200 b <- 0.55 c <- c(0.1, .02, .1, .02)  params = make_parameters_X_SIS(pars = params, b = b, c = c, r = r) params = make_inits_X_SIS(params, S0 = H-I0, I0=I0)"},{"path":[]},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"initial-conditions","dir":"Articles","previous_headings":"Simulation, the Long Way","what":"Initial Conditions","title":"5-3-4 Example","text":"parameters 5-3-4 specified, can generate indices model attach parameter list. Now can set initial conditions model.","code":"params = make_indices(params) y0 = get_inits(params) params <- EggLaying(0, y0, params)"},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"numerical-solution","dir":"Articles","previous_headings":"Simulation, the Long Way","what":"Numerical Solution","title":"5-3-4 Example","text":"Now can pass vector initial conditions, y, parameter list params, function exDE::xDE_diffeqn differential equation solvers deSolve::ode generate numerical trajectory. classes Xpar, MYZpar, Lpar params ensure right methods invoked (dispatched) solve model.","code":"out <- deSolve::ode(y = y0, times = 0:365,                      func = xDE_diffeqn, parms = params, method = \"lsoda\") out1 <- out"},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"plot-output","dir":"Articles","previous_headings":"Simulation, the Long Way","what":"Plot Output","title":"5-3-4 Example","text":"small amount data wrangling made easier data.table package, can plot output.","code":"colnames(out)[params$ix$L[[1]]$L_ix+1] <- paste0('L_', 1:params$nHabitats) colnames(out)[params$ix$MYZ[[1]]$M_ix+1] <- paste0('M_', 1:params$nPatches) colnames(out)[params$ix$MYZ[[1]]$P_ix+1] <- paste0('P_', 1:params$nPatches) colnames(out)[params$ix$MYZ[[1]]$Y_ix+1] <- paste0('Y_', 1:params$nPatches) colnames(out)[params$ix$MYZ[[1]]$Z_ix+1] <- paste0('Z_', 1:params$nPatches) colnames(out)[params$ix$X[[1]]$X_ix+1] <- paste0('X_', 1:params$nStrata)  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Stratification\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Stratification)) +  geom_line() +  facet_wrap(. ~ Component, scales = 'free') +  theme_bw()"},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"using-setup","dir":"Articles","previous_headings":"","what":"Using Setup","title":"5-3-4 Example","text":"create lists parameters values: solve take differences check: Interestingly, differences small:","code":"MYZo = list(  solve_as = \"ode\",   g = 1/12, sigma = 1/12/2,  f = 1/3, q=0.9, nu=c(1/3,1/3,0),  eggsPerBatch = 30,   eip = 12,   M0 = 100,  P0 = 10,  Y0 = 1, Z0 = 0  ) Lo = list(  L0 = 1,  psi = 1/8, phi = 1/8,   theta = c(1/10, 1/20, 1/40, 1/100, 1/10)  ) Xo = list(  I0 = as.vector(0.2*H),  r = 1/200,  b = 0.55,  c = c(0.1, .02, .1, .02) ) EIPo <- list(eip=12) xde_setup(\"mod534\", \"RM\", \"SIS\", \"basic\",                    nPatches = 3, HPop=c(10, 90, 100, 900),                    membership=c(1,1,1,2,2), EIPopts = EIPo,                   MYZopts=MYZo, calK=calK, Xopts=Xo,                    residence=c(2,2,3,3), searchB=searchWtsH,                    TimeSpent=TaR, searchQ = c(7,2,1,8,2), Lopts = Lo) -> mod534 mod534 <- xde_solve(mod534,Tmax=365,dt=1) mod534$outputs$orbits$deout -> out2 approx_equal(tail(out2, 1), tail(out1,1), tol = 1e-5) #>        time   L1   L2   L3   L4   L5 MYZ1 MYZ2 MYZ3 MYZ4 MYZ5 MYZ6 MYZ7 MYZ8 #> [366,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #>        MYZ9 MYZ10 MYZ11 MYZ12   X1   X2   X3   X4   X5   X6   X7   X8 #> [366,] TRUE  TRUE  TRUE  TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE"},{"path":"https://dd-harp.github.io/exDE/articles/human_hmoi.html","id":"differential-equations","dir":"Articles","previous_headings":"","what":"Differential Equations","title":"Hybrid MoI (Multiplicity of Infection) Human Model","text":"equations follows: \\[ \\dot{m_{1}} = h - r_{1}m_{1} \\] \\[ \\dot{m_{2}} = h - r_{2}m_{2} \\] \\(h = b EIR\\), force infection. Prevalence can calculated MoI values : \\[ x_{1} = 1-e^{-m_{1}} \\] \\[ x_{2} = 1-e^{-m_{2}} \\] net infectious probability mosquitoes therefore given : \\[ x = c_{2}x_{2} + c_{1}(x_{1}-x_{2}) \\] \\(c_{1}\\) infectiousness inapparent infections, \\(c_{2}\\) infectiousness patent infections.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/human_hmoi.html","id":"equilibrium-solutions","dir":"Articles","previous_headings":"","what":"Equilibrium solutions","title":"Hybrid MoI (Multiplicity of Infection) Human Model","text":"One way proceed assume \\(m_{2}\\) known, models MoI patent (observable) infections. : \\[ h = r_{2}/m_{2} \\] \\[ m_{1} = h/r_{1} \\] can use calculate net infectious probability, \\(\\kappa = \\beta^{\\top} \\cdot x\\), allowing equilibrium solutions model feed components.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/human_hmoi.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"Hybrid MoI (Multiplicity of Infection) Human Model","text":"run simple example 3 population strata equilibrium. use exDE::make_parameters_X_hMoI set parameters. Please note runs human population component users read fully worked example run full simulation. use null (constant) model human demography (\\(H\\) constant time). \\(H\\) appear equations , must specified model bloodfeeding (\\(\\beta\\)) relies \\(H\\) compute consistent values.","code":"library(exDE) library(deSolve) library(data.table) library(ggplot2)"},{"path":"https://dd-harp.github.io/exDE/articles/human_hmoi.html","id":"the-long-way","dir":"Articles","previous_headings":"","what":"The Long Way","title":"Hybrid MoI (Multiplicity of Infection) Human Model","text":", build model step--step.","code":"nStrata <- 3 H <- c(100, 500, 250) residence = rep(1,3)  searchWtsH = rep(1,3)  b <- 0.55 c1 <- 0.05 c2 <- 0.25 r1 <- 1/250 r2 <- 1/50 TaR <- matrix(data = 1, nrow = 1, ncol = nStrata)  m20 <- 1.5 h <- r2*m20 m10 <- h/r1  EIR <- h/b params <- make_parameters_xde() params$nStrata = nStrata params$nVectors = 1  params$nHosts = 1 params$nPatches = 1  params$eir = rep(EIR, 3) params$EIR = list()  F_eir = function(t, pars){   pars$EIR[[1]] = pars$eir }  params = make_parameters_demography_null(pars = params, H=H)   params = setup_BloodFeeding(params, 1, 1, residence=residence, searchWts=searchWtsH)  params$BFpar$TaR[[1]][[1]]=TaR params = make_parameters_X_hMoI(pars = params, b = b, c1 = c1, c2 = c2, r1 = r1, r2 = r2) params = make_inits_X_hMoI(pars = params, rep(m10, nStrata), rep(m20, nStrata))  params = make_indices(params) y0 <- get_inits(params)  out <- deSolve::ode(y = y0, times = c(0, 365), func = xDE_diffeqn_cohort,                      parms = params, method = 'lsoda', F_eir = F_eir)  out1 <- out colnames(out)[params$ix$X[[1]]$m1_ix+1] <- paste0('m1_', 1:params$nStrata) colnames(out)[params$ix$X[[1]]$m2_ix+1] <- paste0('m2_', 1:params$nStrata)  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Strata\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Strata)) +   geom_line() +   facet_wrap(Strata ~ Component, scales = 'free') +   theme_bw()"},{"path":"https://dd-harp.github.io/exDE/articles/human_hmoi.html","id":"using-setup","dir":"Articles","previous_headings":"","what":"Using Setup","title":"Hybrid MoI (Multiplicity of Infection) Human Model","text":"","code":"Xo = list(b=0.55, c1=0.05, c2=0.25, r1=1/250, r2=1/50, m20=1.5) h = with(Xo, r2*m20)  Xo$m10 = with(Xo, h/r1)   Hpop = c(100, 500, 250) h/b #> [1] 0.05454545 fF_eir1 = function(EIR){return(function(t, pars){EIR})}  F_eir1 = fF_eir1(EIR) xde_setup_cohort(F_eir1, Xname=\"hMoI\", HPop=Hpop, Xopts = Xo) ->test_hMoI xde_solve(test_hMoI, 365, 365)$outputs$orbits$deout -> out2 approx_equal(out2, out1) #>      time   X1   X2   X3   X4   X5   X6 #> [1,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [2,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE"},{"path":"https://dd-harp.github.io/exDE/articles/human_sip.html","id":"differential-equations","dir":"Articles","previous_headings":"","what":"Differential Equations","title":"SIP (Susceptible-Infected-Prophylaxis) Human Model","text":"equations follows: \\[ \\dot{X} = \\mbox{diag}((1-\\rho)bEIR)\\cdot (H-X-P) - (r+\\xi)X \\] \\[ \\dot{P} = \\mbox{diag}(\\rho b EIR) \\cdot (H-X-P) + \\xi(H-P) - \\eta P \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/human_sip.html","id":"equilibrium-solutions","dir":"Articles","previous_headings":"","what":"Equilibrium solutions","title":"SIP (Susceptible-Infected-Prophylaxis) Human Model","text":", assume \\(H\\) \\(X\\) known, set \\(\\xi=0\\), solve \\(EIR\\) \\(P\\). \\[ P = \\mbox{diag}(1/\\eta) \\cdot \\mbox{diag}(\\rho/(1-\\rho)) \\cdot rX \\] \\[ EIR = \\mbox{diag}(1/b) \\cdot \\mbox{diag}(1/(1-\\rho)) \\cdot \\left( \\frac{rX}{H-X-P} \\right) \\] Given \\(EIR\\) can solve mosquito population given rise equilibrium values.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/human_sip.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"SIP (Susceptible-Infected-Prophylaxis) Human Model","text":"run simple example 3 population strata equilibrium. use exDE::make_parameters_X_SIP set parameters. Please note runs human population component users read fully worked example run full simulation. use null (constant) model human demography (\\(H\\) constant time).","code":"library(exDE) library(deSolve) library(data.table) library(ggplot2)"},{"path":"https://dd-harp.github.io/exDE/articles/human_sip.html","id":"the-long-way","dir":"Articles","previous_headings":"Example","what":"The Long Way","title":"SIP (Susceptible-Infected-Prophylaxis) Human Model","text":"","code":"nStrata <- 3 H <- c(100, 500, 250) residence <- rep(1,3)  searchWtsH <- rep(1,3)  I <- c(20, 120, 80) b <- 0.55 c <- 0.15 r <- 1/200 eta <- c(1/30, 1/40, 1/35) rho <- c(0.05, 0.1, 0.15) xi <- rep(0, 3)  TaR <- matrix(data = 1,nrow = 1, ncol = nStrata)  P <- diag(1/eta) %*% diag(rho/(1-rho)) %*% (r*I) EIR <- diag(1/b, nStrata) %*% diag(1/(1-rho)) %*% ((r*I)/(H-I-P)) params <- make_parameters_xde() params$nStrata = nStrata params$nPatches = 1  params$nHosts = 1   params$eir = EIR params$EIR = list()  F_eir = function(t, pars){   pars$EIR[[1]] = params$eir }  params = make_parameters_demography_null(pars = params, H=H)   params = setup_BloodFeeding(params, 1, 1, residence=residence, searchWts =searchWtsH)  params$BFpar$TaR[[1]][[1]]=TaR  params = make_parameters_X_SIP(pars = params, b = b, c = c, r = r, rho = rho, eta = eta, xi=xi) params = make_inits_X_SIP(pars = params, H-I-P, I, as.vector(P)) params = make_indices(params) y0 <- get_inits(params) out <- deSolve::ode(y = y0, times = c(0, 365), xDE_diffeqn_cohort, parms = params, method = 'lsoda', F_eir = F_eir)  out1<- out colnames(out)[params$ix$X[[1]]$S_ix+1] <- paste0('S_', 1:params$nStrata) colnames(out)[params$ix$X[[1]]$I_ix+1] <- paste0('I_', 1:params$nStrata) colnames(out)[params$ix$X[[1]]$P_ix+1] <- paste0('P_', 1:params$nStrata)  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Strata\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Strata)) +   geom_line() +   facet_wrap(. ~ Component, scales = 'free') +   theme_bw()"},{"path":"https://dd-harp.github.io/exDE/articles/human_sip.html","id":"using-setup","dir":"Articles","previous_headings":"Example","what":"Using Setup","title":"SIP (Susceptible-Infected-Prophylaxis) Human Model","text":"use xde_setup_cohort must set function F_eir returns value EIR computed :","code":"Xo = list(b=0.55, c=0.15, r=1/200,            eta = c(1/30, 1/40, 1/35), rho = c(0.05, .1, 0.15),            xi = rep(0,3),            I0=I, P0=as.vector(P)) Hpop = c(100, 500, 250) fF_eir1 = function(EIR){return(function(t, pars){EIR})}  F_eir1 = fF_eir1(EIR) xde_setup_cohort(F_eir1, Xname=\"SIP\", HPop=Hpop, Xopts = Xo) -> test_SIP xde_solve(test_SIP, 365, 365)$outputs$orbits$deout -> out2 approx_equal(out2,out1)  #>      time   X1   X2   X3   X4   X5   X6   X7   X8   X9 #> [1,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [2,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE"},{"path":"https://dd-harp.github.io/exDE/articles/human_sis.html","id":"differential-equations","dir":"Articles","previous_headings":"","what":"Differential Equations","title":"SIS (Susceptible-Infected-Susceptible) Human Model","text":"subdivide population susceptible (\\(S\\)) infected infectious (\\(\\)) individuals, total population \\(H = S+.\\) assume force infection (\\(h\\), FoI) linearly proportional EIR: \\(h = b \\times EIR.\\) general form, births (\\(B(H)\\)) deaths (per-capita rate \\(\\mu\\)), generalized SIS dynamics : \\[ \\begin{array}{rl} \\dot{S} &= -h S + rI + B(H) -\\mu S\\\\ \\dot{} &= h S  - rI - \\mu \\end{array} \\] demographic change, SIS model can rewritten single equation: \\[ \\dot{} = h (H-) - rI \\] Even simplified form, assuming population stratified, variables parameter vectors length nStrata.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/human_sis.html","id":"equilibrium-solutions","dir":"Articles","previous_headings":"","what":"Equilibrium Solutions","title":"SIS (Susceptible-Infected-Susceptible) Human Model","text":"typical situation using model \\(H\\) (total population size strata) \\(X\\) (number infectious persons strata) known census survey data. interest find value \\(EIR\\) (Entomological Inoculation Rate) leads prevalence equilibrium. \\[ 0 = \\mbox{diag}(bEIR) \\cdot (H-) - rI \\] \\[ rI = \\mbox{diag}(b) \\cdot \\mbox{diag}(EIR) \\cdot (H-) \\] \\[ \\frac{rI}{H-} = \\mbox{diag}(b) \\cdot \\mbox{diag}(EIR) \\] \\[ \\mbox{diag}(1/b) \\cdot \\left(\\frac{rI}{H-}\\right) = EIR \\] Note final line, \\(EIR\\) column vector dimension \\(n\\) due operations left. element gives per-capita rate individuals population strata receive potentially infectious bites (summing across places visit).","code":""},{"path":"https://dd-harp.github.io/exDE/articles/human_sis.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"SIS (Susceptible-Infected-Susceptible) Human Model","text":"run simple example 3 population strata equilibrium. use exDE::make_parameters_X_SIS set parameters. Please note runs human population component users read fully worked example run full simulation. use null (constant) model human demography (\\(H\\) constant time).","code":"library(exDE) library(deSolve) library(data.table) library(ggplot2)"},{"path":"https://dd-harp.github.io/exDE/articles/human_sis.html","id":"the-long-way","dir":"Articles","previous_headings":"Example","what":"The Long Way","title":"SIS (Susceptible-Infected-Susceptible) Human Model","text":"set systems differential equations, must set values parameters.","code":"nStrata <- 3 H <- c(100, 500, 250) residence <- rep(1,3)  searchWtsH <- rep(1,3)  I <- c(20, 120, 80) b <- rep(0.55, nStrata)  c <- rep(0.15, nStrata)  r <- rep(1/200, nStrata)  TaR <- matrix(data = 1,nrow = 1, ncol = nStrata)  EIR <- diag(1/b, nStrata) %*% ((r*I)/(H-I)) params <- make_parameters_xde() params$nStrata = nStrata params$nPatches = 1 params$nHosts = 1  params$eir = EIR params$EIR = list()   params$eir = as.vector(EIR) F_eir = function(t, pars){   pars$EIR[[1]] = pars$eir }  params = make_parameters_demography_null(pars = params, H=H)   params = setup_BloodFeeding(params, 1, 1, residence=residence, searchWts=searchWtsH)  params$BFpar$TaR[[1]][[1]]=TaR  params = make_parameters_X_SIS(pars = params, b = b, c = c, r = r)  params = make_inits_X_SIS(pars = params, H-I, I)  params = make_indices(params) y0 <- get_inits(params)  out <- deSolve::ode(y = y0, times = c(0, 365), xDE_diffeqn_cohort,                      parms = params, method = 'lsoda', F_eir = F_eir)  out1 <- out colnames(out)[params$ix$X$S_ix+1] <- paste0('S_', 1:params$nStrata) colnames(out)[params$ix$X$I_ix+1] <- paste0('I_', 1:params$nStrata)  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Strata\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Strata)) +   geom_line() +   facet_wrap(. ~ Component, scales = 'free') +   theme_bw()"},{"path":"https://dd-harp.github.io/exDE/articles/human_sis.html","id":"using-setup","dir":"Articles","previous_headings":"Example","what":"Using Setup","title":"SIS (Susceptible-Infected-Susceptible) Human Model","text":"developed utilities setting models. pass parameter values initial values lists: use xde_setup_cohort must set function F_eir returns value EIR computed :","code":"Xo = list(b=0.55, c=0.15, r=1/200, I0 = I) Hpop = c(100, 500, 250) fF_eir1 = function(EIR){return(function(t, pars){EIR})}  F_eir1 = fF_eir1(EIR) xde_setup_cohort(F_eir1, Xname=\"SIS\", HPop=Hpop, Xopts = Xo) -> test_SIS xde_solve(test_SIS, 365, 365)$outputs$orbits$deout -> out2 approx_equal(out2,out1) #>      time   X1   X2   X3   X4   X5   X6 #> [1,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [2,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE"},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Modular Forms for Disease Dynamics","text":"Modular forms disease dynamics stylized ways writing dynamical systems emphasize modular structure. mathematical framework building models malaria dynamics control (mosquito-borne pathogens) described Spatial Dynamics Malaria Transmission, framework implemented exDE. forms describe rewrite models closely resemble implementation exDE, makes possible relate written equations computed code. (Also, see closely related vignette Understanding exDE.)","code":""},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"the-modular-form","dir":"Articles","previous_headings":"","what":"The Modular Form","title":"Modular Forms for Disease Dynamics","text":"illustrate writing Ross-Macdonald model modular form (Figure 1). classical form, model: \\[ \\begin{array}{rl} dX/dt &= b e^{-gn}fq \\frac YH (H-X) - r X \\\\ dY/dt &= c \\frac XH (M-Y) - g Y \\end{array}\\] model explained . Figure 1 - Diagram Ross-Macdonald model written modular form.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"parasite-infection-dynamics-in-humans-cal-x","dir":"Articles","previous_headings":"The Modular Form","what":"Parasite Infection Dynamics in Humans, \\(\\cal X\\)","title":"Modular Forms for Disease Dynamics","text":"equation describing human infections written following way: \\[ dI/dt = h (H-) - r \\] : \\(\\) density infected infectious humans; \\(H\\) density humans; \\(h\\) force infection (FoI), number infections, per perspon, per day; related daily entomological inoculation rate (dEIR). \\(r\\) clearance rate, number infections clear, per infected person, per day.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"parasite-infection-dynamics-in-mosquitoes-cal-yz","dir":"Articles","previous_headings":"The Modular Form","what":"Parasite Infection Dynamics in Mosquitoes, \\(\\cal YZ\\)","title":"Modular Forms for Disease Dynamics","text":"Similarly, equation describing infected mosquitoes following: \\[ dY/dt = \\kappa (M-Y) - g Y \\] : \\(Y\\) density infected mosquitoes; \\(M\\) density mosquitoes; \\(f\\) overall mosquito blood feeding rate, number human blood meals, per mosquito, per day; \\(q\\) human fraction; human blood feeding fraction blood feeding; \\(\\kappa\\) net infectiousness (NI) humans, probability mosquito become infected blood feeding human; related density infected humans. \\(g\\) mosquito death rate, number mosquitoes dying, per mosquito, per day;","code":""},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"blood-feeding","dir":"Articles","previous_headings":"The Modular Form","what":"Blood Feeding","title":"Modular Forms for Disease Dynamics","text":"two terms, FoI (\\(h\\)) NI (\\(\\kappa\\)), equations rely information comes equation. compute , need construct deal concept mixing, denote \\(\\beta\\). generic form, computation terms defines blood feeding model, interface \\(\\cal YZ\\) \\(\\cal X.\\)","code":""},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"force-of-infection-foi","dir":"Articles","previous_headings":"The Modular Form > Blood Feeding","what":"Force of Infection (FoI)","title":"Modular Forms for Disease Dynamics","text":"FoI \\(h\\) must related density infected mosquitoes. compute several steps. First, Ross-Macdonald model, density blood feeding mosquitoes given formula: \\[Z = F_Z(Y) = e^{-gn} Y\\] \\(n\\) extrinsic incubation period (EIP) Next, need compute EIR, computed distributing infective bites among humans. model, mixing uniform \\(\\beta = 1/H\\), write: \\[ E = \\beta \\cdot fqZ = \\frac {fqZ}H\\] finally, must compute FoI, draws information many different sources, \\[ h = F_h(E, ...) = b E.\\] \\(b\\) fraction infective bites cause infection;","code":""},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"net-infectiousness-ni","dir":"Articles","previous_headings":"The Modular Form > Blood Feeding","what":"Net Infectiousness (NI)","title":"Modular Forms for Disease Dynamics","text":"NI \\(\\kappa\\) must related density infected humans. Ross-Macdonald model, effective density infected humans : \\[X = F_X() = cI\\] \\(c\\) probability mosquito become infected blood feeding infected human. net infectiousness computed infective density averaged biting among humans. reasons become clear later, call \\(\\beta^T = 1/H\\): \\[\\kappa =  \\beta^T \\cdot X = \\frac XH\\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"computation","dir":"Articles","previous_headings":"","what":"Computation","title":"Modular Forms for Disease Dynamics","text":"solve equations, need write functions compute derivatives. using R package deSolve, derivative function constrained form: exDE, equations solved computing terms derivatives separately. Transmission(t,y,pars) computes three terms required compute parasite transmission blood feeding. stored main model object pars: pars$beta pars$EIR pars$NI Exposure(t, y, pars) computes FoI EIR model exposure stores pars$FoI instead developing models like RMv1, implemented code syle RMv2:","code":"RMv1 <- function(t, y, pars) {   with(pars,{       foi = b*exp(-g*n)*Y/H       kappa = c*I/H       dX = foi*(H-I) - r*I       dY = a*kappa*(M-Y) - g*Y        return(list(dX, dY))   }) } RMv2 <- function(t, y, pars) {   with(pars,{       pars = Transmission(t, y, pars)       pars = Exposure(t, y, pars)       dX = dXdt(t, y, pars)        dY = dMYZdt(t, y, pars)        return(list(dX, dY))   }) }"},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"full-modularity","dir":"Articles","previous_headings":"","what":"Full Modularity","title":"Modular Forms for Disease Dynamics","text":"full structure computation exDE diagrammed Figure 2 easily examined corresponding code. One advantage modular notation possible set describe reasonably complex models fairly simple scripts. vignette 5-3-4 Example shows works. Figure 2","code":""},{"path":"https://dd-harp.github.io/exDE/articles/spat_metric.html","id":"human-movement","dir":"Articles","previous_headings":"","what":"Human Movement","title":"Spatial Metrics","text":"start fundamental matrix \\(\\Psi\\) dimension \\(p\\times n\\) , column \\(\\) gives distribution time risk strata places (rows). strata considered potentially risk 100% time, columns sum one, convention adopt document. \\(\\Psi_{ji}\\) fraction time strata \\(\\) spends patch \\(j\\).","code":""},{"path":"https://dd-harp.github.io/exDE/articles/spat_metric.html","id":"ambient-human-population","dir":"Articles","previous_headings":"","what":"Ambient Human Population","title":"Spatial Metrics","text":"Let \\(H\\) length \\(n\\) column vector giving population size strata. Let \\(w_{f}\\) length \\(n\\) column vector giving biting weights strata (null value \\(1\\)). want know \\(W\\), length \\(p\\) column vector tells us many people patch (summing strata ). \\[ W =\\begin{bmatrix} \\sum_{} \\Psi_{1i}w_{f1}H_{} \\\\ \\vdots \\\\ \\sum_{} \\Psi_{pi}w_{fi}H_{} \\end{bmatrix} = \\Psi \\cdot w_{f} H \\] element \\(W\\) gives total weighted person-time spent strata location.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/spat_metric.html","id":"biting-distribution-matrix","dir":"Articles","previous_headings":"","what":"Biting Distribution Matrix","title":"Spatial Metrics","text":"biting distribution matrix \\(\\beta\\) \\(n \\times p\\) matrix central formulating mathematically consistent models bloodfeeding, , extension, consistent models mosquito-borne pathogen transmission. given mathematically : \\[ \\beta = \\mbox{diag}(w_{f}) \\cdot \\Psi^{\\top} \\cdot \\mbox{diag}(1/W) \\] can written component-wise : \\[ \\beta = \\begin{bmatrix} \\frac{\\Psi_{11}w_{f1}}{\\sum_{}\\Psi_{1i}w_{fi}H_{}} & \\cdots & \\frac{\\Psi_{p1}w_{f1}}{\\sum_{}\\Psi_{pi}w_{fi}H_{}} \\\\ \\vdots & & \\vdots \\\\ \\frac{\\Psi_{1n}w_{fn}}{\\sum_{}\\Psi_{1i}w_{fi}H_{}} & \\cdots & \\frac{\\Psi_{pn}w_{fn}}{\\sum_{}\\Psi_{pi}w_{fi}H_{}} \\end{bmatrix} \\] Now can get clearer impression \\(\\beta_{ij}\\) . probability bite mosquitoes patch \\(j\\) lands particular person strata \\(\\). Another way say proportion person-time spent single person strata \\(\\) patch \\(j\\), person-time spent patch. wanted look matrix whose columns sum unity elements give probability bite taken ambient population patch \\(j\\) land strata \\(\\), look following matrix: \\[ \\mbox{diag}(H) \\cdot \\beta \\] operation effect multiplying column \\(\\beta\\) diagonal matrix left, columns sum one (column sums \\(\\Psi\\), case total time risk \\(< 1\\)). Likewise want recover \\(\\Psi^{\\top}\\), \\(n \\times p\\) matrix whose rows describe strata distributes time across patches, one can simply multiply right \\(\\mbox{diag}(W)\\) effect multiplying column \\(\\beta\\) element diagonal \\(\\mbox{diag}(W)\\). \\[ \\beta \\cdot \\mbox{diag}(W) \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/spat_metric.html","id":"human-transmitting-capacity-htc","dir":"Articles","previous_headings":"","what":"Human transmitting capacity (HTC)","title":"Spatial Metrics","text":"Human transmitting capacity vector \\(D\\) length \\(n\\), element gives number net infectious days infected individual strata. homogeneous SIS model, simply: \\[ D = \\frac{c}{r} \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/spat_metric.html","id":"parasite-dispersal-by-mosquitoes","dir":"Articles","previous_headings":"","what":"Parasite dispersal by mosquitoes","title":"Spatial Metrics","text":"parasite dispersal mosquitoes matrix, \\(\\mathcal{V}\\) spatial analogue vectorial capacity, expected number humans infected per infected human, per day, assuming perfect transmission efficiency. \\[ \\mathcal{V} = fq\\Omega^{-1} \\cdot e^{-\\Omega\\tau} \\cdot \\mbox{diag}\\left(\\frac{fqM}{W}\\right) \\] can understood going right left. matrix \\(\\mbox{diag}\\left(\\frac{fqM}{W}\\right)\\) \\(p\\times p\\) matrix, diagonal giving numbers bloodmeals taken person patch, per day. Multiplying left \\(e^{-\\Omega\\tau}\\) effect multiplying column matrix left corresponding element diagonal matrix right. intermediate matrix columns describe bites/person patch distributed across patches extrinsic incubation period, accounting mortality period. final multiplication left distributes bites EIP passed. single patch, formula becomes: \\[ \\frac{fq}{g} e^{-g\\tau}fq\\frac{M}{H} \\] equivalent (substituting \\(H=W\\)) classic formula Smith McKenzie (2004): \\(\\frac{fq}{g}e^{-g\\tau}fq\\frac{M}{H}\\).","code":""},{"path":"https://dd-harp.github.io/exDE/articles/spat_metric.html","id":"parasite-dispersal-by-humans","dir":"Articles","previous_headings":"","what":"Parasite dispersal by humans","title":"Spatial Metrics","text":"\\[ \\mathcal{D} = \\mbox{diag}\\left(W \\right) \\cdot \\beta^T \\cdot \\mbox{diag}\\left(bDH\\right) \\cdot \\beta \\] can first examine multiplication \\(\\mbox{diag}\\left(bDH\\right) \\cdot \\beta\\) right. effect multiplying column \\(\\beta\\) diagonal \\(\\mbox{diag}\\left(bDH\\right)\\). results \\(n\\times p\\) matrix whose columns give distribution potentially transmitting person-time (\\(\\frac{bc}{r}\\)) person strata contributes patch. \\(p\\times p\\) matrix. left \\(\\mbox{diag}\\left(W \\right) \\cdot \\beta^T\\) multiplies column \\(\\beta^T\\) diagonal matrix; effect recovering original movement matrix \\(\\Psi\\). multiplying intermediate matrix produced preceding section left distributes potentially-transmitting person time across patches. Therefore \\(\\)-th column \\(\\mathcal{D}\\) describes potentially infectious person-time person infected \\(\\) distributed across patches. 1 patch, 1 strata case, simplifies considerably : \\[ \\mathcal{D} = \\frac{bc}{r} \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/spat_metric.html","id":"parasite-dispersal-through-one-parasite-generation","dir":"Articles","previous_headings":"","what":"Parasite Dispersal through one Parasite Generation","title":"Spatial Metrics","text":"One way look parasite dispersal look parasites dispersed one parasite generation. can done mosquito mosquito, human human. show equation parasite dispersal generation, beginning ending human host. \\[ \\mathcal{R} =   b \\beta \\cdot {\\cal V}  \\cdot \\mbox{diag}\\left(W \\right) \\cdot \\beta^T  \\cdot \\mbox{diag}\\left(DH\\right) \\] \\(\\mathcal{R}\\) \\(n\\times n\\) matrix, columns describe infections starting strata disseminated among strata one generation. can learn interpret equation walking left right. \\(\\mbox{diag}\\left(W \\right) \\cdot \\beta^T \\cdot \\mbox{diag}\\left(DH\\right)\\) produces \\(p\\times n\\) matrix describes infectious person-time strata spread across patches. Multiplication \\(\\mathcal{V}\\) describes infectious person-time transformed potentially infectious bites mosquitoes, distributed space accounting mortality EIP. Final multiplication \\(\\beta\\) \\(b\\) takes account persons contact infectious bites, transmission efficiency back human hosts. , can take 1 patch, 1 strata case see formula simplifies: \\[ \\frac{bc}{r} \\cdot \\frac{fq}{g} e^{-g\\tau}fq\\frac{M}{H} \\] precisely formula \\(R_{0}\\) Smith McKenzie (2004). Therefore \\(\\mathcal{R}\\) “logical” spatial version threshold metric. track parasite dispersal mosquitoes mosquitoes arrive \\(p\\times p\\) matrix: \\[ \\mathcal{Z} = e^{-\\Omega\\tau} \\cdot \\mbox{diag}\\left( \\frac{fq M}{W} \\right) \\cdot {\\cal D} \\cdot  fq\\Omega^{-1} \\] 1 patch 1 strata case becomes equation \\(\\mathcal{R}\\).","code":""},{"path":"https://dd-harp.github.io/exDE/articles/spat_metric.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"Spatial Metrics","text":"demonstrate calculate metrics using 5-3-4 example. can visualize matrices heatmaps.","code":"library(exDE) library(ggplot2) l <- 5 p <- 3 n <- 4  calN <- matrix(   data = c(1,1,1,0,0,            0,0,0,1,1,            0,0,0,0,0),    nrow = p, ncol = l, byrow = TRUE )   xi <- matrix(c(.7, .2, .1, .8, .2), 5, 1)  calU <- t(calN %*% diag(as.vector(xi)))  g <- rep(1/12, p)  sigma <- rep(1/12/2, p)  calK <- t(matrix(   c(c(0, .6, .3),      c(.4, 0, .7),      c(.6, .4, 0)), 3, 3)) f <- rep(1/3, p)  q <- rep(0.9, p)  tau <- 12  M <- rep(100, p)  Omega <- diag(g) + (diag(1,p)-calK) %*% diag(sigma) Lambda <- Omega %*% M  H <- matrix(c(10,90, 100, 900), 4, 1) X <- as.vector(0.2*H) r <- rep(1/200, n) b <- rep(0.55, n) c <- c(0.1, .02, .1, .02)  calJ <- t(matrix(   c(c(0,0,0,0),     c(1,1,0,0),     c(0,0,1,1)), n, p ))  Theta <- t(matrix(   c(c(0.01,0.01,0.001,0.001),     c(.95,.92,.04,.02),     c(.04,.02,.959,.929)), n, p ))  W <- Theta %*% H beta <- t(Theta) %*% diag_inverse(W)  D <- c/r  calV <- metric_calV(f = f, q = q, Omega = Omega, tau = tau, M = M, W = W) calD <- metric_calD(W = W, beta = beta, b = b, D = D, H = H) calR <- metric_calR(b = b, beta = beta, calV = calV, W = W, D = D, H = H) calZ <- metric_calZ(Omega = Omega, tau = tau, f = f, q = q, M = M, W = W, calD = calD) calV_df <- data.frame(   value = as.vector(calV),   x = rep(1:nrow(calV), times = nrow(calV)),   y = rep(1:nrow(calV), each = nrow(calV)) )  ggplot(calV_df, aes(x=x,y=y,fill=log(value))) +     geom_raster() +     scale_y_reverse() +     guides(fill = 'none') +     theme(axis.title = element_blank())"},{"path":"https://dd-harp.github.io/exDE/articles/vc_lemenach.html","id":"parameters","dir":"Articles","previous_headings":"","what":"Parameters","title":"ITN-based Vector Control","text":"case study use simple model 3 patches, 3 population strata, 3 aquatic habitats. usual, set parameter values compute values state variables equilibrium. part equilibrium calculation must compute \\(\\Upsilon(0) = \\exp\\left(-\\int_{-\\tau}^{0} \\Omega(s) ds \\right)\\); value integrated mosquito demography matrix initial time point. simplify things, simply assume conditions constant prior \\(t=0\\) \\(\\Upsilon(0) = e^{-\\Omega\\tau}\\).","code":"nPatches <- 3 nVectors <- 1 nStrata <- 3 nHabitats <- 3  # human parameters b <- 0.55 c <- 0.15 r <- 1/200  wf <- rep(1, nStrata)  pfpr <- runif(n = nStrata, min = 0.25, max = 0.35) Hpop <- rpois(n = nStrata, lambda = 1000) X <- rbinom(n = nStrata, size = Hpop, prob = pfpr)  residence = c(1:3) searchWtsH = rep(1,3)   TaR <- matrix(   data = c(     0.9, 0.05, 0.05,     0.05, 0.9, 0.05,     0.05, 0.05, 0.9   ), nrow = nStrata, ncol = nPatches, byrow = T ) TaR <- t(TaR)  f <- 0.3  q <- 0.9  g <- 1/10  sigma <- 1/100  nu <- 1/2  eggsPerBatch <- 30 eip <- 11 calK = make_calK(nPatches, \"herethere\")"},{"path":"https://dd-harp.github.io/exDE/articles/vc_lemenach.html","id":"equilibrium","dir":"Articles","previous_headings":"","what":"Equilibrium","title":"ITN-based Vector Control","text":"Now compute equilibrium conditions adult mosquitoes human populations, PfPR human population maintained input levels conditions unchanging. Given equilibrium value \\(\\Lambda\\) required sustain mosquito populations level sufficient maintain transmission level PfPR, well values \\(\\psi\\) (maturation rate) \\(\\phi\\) (density independent mortality), compute equilibrium values \\(L\\) (aquatic mosquito density) \\(\\theta\\) (density dependent mortality).","code":"# derived EIR to sustain equilibrium pfpr EIR <- diag(1/b, nStrata) %*% ((r*X) / (Hpop - X))  # ambient pop W <- TaR %*% Hpop  # biting distribution matrix beta <- diag(wf) %*% t(TaR) %*% diag(1/as.vector(W), nPatches)  # kappa kappa <- t(beta) %*% (X*c)  Omega <- make_Omega(g = g, sigma = sigma, K = calK, nPatches = nPatches) Omega_inv <- solve(Omega) Upsilon <- expm::expm(-Omega * eip) Upsilon_inv <- expm::expm(Omega * eip)  # equilibrium solutions Z <- diag(1/(f*q), nPatches) %*% ginv(beta) %*% EIR MY <- diag(1/as.vector(f*q*kappa), nPatches) %*% Upsilon_inv %*% Omega %*% Z Y <- Omega_inv %*% (diag(as.vector(f*q*kappa), nPatches) %*% MY) M <- MY + Y P <- solve(diag(f, nPatches) + Omega) %*% diag(f, nPatches) %*% M Lambda <- Omega %*% M # aquatic habitat membership matrix (assume 1 habitat per patch) calN <- matrix(0, nPatches, nHabitats) diag(calN) <- 1  # egg dispersal matrix (assume 1 habitat per patch) calU <- matrix(0, nHabitats, nPatches) diag(calU) <- 1  psi <- 1/10 phi <- 1/12 eta <- as.vector(calU %*% (M * nu * eggsPerBatch))  alpha <- as.vector(solve(calN) %*% Lambda) L <- alpha/psi theta <- (eta - psi*L - phi*L)/(L^2)"},{"path":"https://dd-harp.github.io/exDE/articles/vc_lemenach.html","id":"setup","dir":"Articles","previous_headings":"","what":"Setup","title":"ITN-based Vector Control","text":"Now state variables solved equilibrium, can set parameters components system. use null model human demographic dynamics, assumes \\(H\\) constant time. ran model point, get baseline. Instead, set time-varying function compute coverage ITNs time point. use sine curve period 365 days goes 0 1 period, phase shifted 0 returns 0. function also returns 0 \\(t<0\\). must function takes single argument t (time) returns scalar value. use null model human demographic dynamics, assumes \\(H\\) constant time.","code":"# adult mosquito parameters Xo = list(b=b, c=c, r=r, X0=X)  Lo = list(psi=psi, phi=phi, theta=theta, L0=L)  MYZo = list(f=f, q=q, g=g, sigma=sigma,              nu=nu, eggsPerBatch=eggsPerBatch, eip=eip,              M0=M, P0=P, Y0=Y, Z0=Z) xde_setup(MYZname=\"RM\", Xname=\"SIS\", Lname=\"basic\",            nPatches=3, HPop=Hpop, membership=c(1:3), MYZopts=MYZo, calK=calK,            Xopts=Xo, residence=1:3, searchB=rep(1,3),            TimeSpent =TaR, searchQ=rep(1,3), Lopts=Lo) -> itn_mod itn_mod <- setup_control(itn_mod) # ITN coverage ITN_cov <- function(t) {ifelse(t < 0, 0, (sin(2*pi*(t-365/4) / 365) + 1) / 2)} itn_mod = setup_itn_lemenach(itn_mod, phi = ITN_cov) xde_solve(itn_mod, 5*365) -> itn_mod itn_mod$outputs$orbits$deout -> out"},{"path":"https://dd-harp.github.io/exDE/articles/vc_lemenach.html","id":"plot","dir":"Articles","previous_headings":"","what":"Plot","title":"ITN-based Vector Control","text":"can plot output study effects seasonal ITN coverage state variables. see total parous mosquito densities \\(M\\) \\(G\\) now vary sinusoidal manner coverage changes, \\(L\\), larval density, number ovipositing mosquitoes changes. addition increasing mosquito mortality, ITNs also decrease feeding rate proportion bloodmeals taken humans due repellency effect, see densities infected infectious mosquitoes (\\(Y\\) \\(Z\\)) steadily decrease time longer sufficient bloodmeals taken sustain prevalence. similar pattern appears human prevalence \\(X\\), slower dynamics due slow recovery rate untreated infection.","code":"colnames(out)[itn_mod$ix$L[[1]]$L_ix+1] <- paste0('L_', 1:itn_mod$nHabitats) colnames(out)[itn_mod$ix$MYZ[[1]]$M_ix+1] <- paste0('M_', 1:itn_mod$nPatches) colnames(out)[itn_mod$ix$MYZ[[1]]$P_ix+1] <- paste0('P_', 1:itn_mod$nPatches) colnames(out)[itn_mod$ix$MYZ[[1]]$Y_ix+1] <- paste0('Y_', 1:itn_mod$nPatches) colnames(out)[itn_mod$ix$MYZ[[1]]$Z_ix+1] <- paste0('Z_', 1:itn_mod$nPatches) colnames(out)[itn_mod$ix$X[[1]]$X_ix+1] <- paste0('X_', 1:itn_mod$Hpar[[1]]$nStrata)  out <- out[, -c(itn_mod$ix$MYZ[[1]]$sigma_ix+1)] out <- out[, -c(itn_mod$ix$MYZ[[1]]$g_ix+1)] out <- out[, -c(itn_mod$ix$MYZ[[1]]$fqkappa_ix+1)] out <- out[, -c(itn_mod$ix$MYZ[[1]]$Upsilon_ix+1)]  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Stratification\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Stratification)) +   geom_line() +   facet_wrap(. ~ Component, scales = 'free') +   theme_bw()"},{"path":"https://dd-harp.github.io/exDE/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Sean L. Wu. Author, maintainer. David L. Smith. Author.","code":""},{"path":"https://dd-harp.github.io/exDE/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Wu S, Henry J, Citron D, Ssebuliba D, Nsumba J, Sánchez C. H, Brady O, Guerra C, García G, Carter , Ferguson H, Afolabi B, Hay S, Reiner R, Kiware S, Smith D (2022). “Spatial Dynamics Malaria Transmission.” medRxiv. doi:10.1101/2022.11.07.22282044, https://www.medrxiv.org/content/10.1101/2022.11.07.22282044v1.","code":"@Article{,   title = {Spatial Dynamics of Malaria Transmission},   author = {Sean L. Wu and John M. Henry and Daniel T. Citron and Doreen M. Ssebuliba and Juliet N. Nsumba and Héctor M. {Sánchez C.} and Oliver J. Brady and Carlos A. Guerra and Guillermo A. García and Austin R. Carter and Heather M. Ferguson and Bakare E. Afolabi and Simon I. Hay and Robert C. Reiner and Samson Kiware and David L. Smith},   journal = {medRxiv},   year = {2022},   publisher = {Cold Spring Harbor Laboratory Press},   url = {https://www.medrxiv.org/content/10.1101/2022.11.07.22282044v1},   doi = {10.1101/2022.11.07.22282044}, }"},{"path":[]},{"path":"https://dd-harp.github.io/exDE/index.html","id":"what-is-exde","dir":"","previous_headings":"","what":"What is exDE?","title":"Extensible Differential Equations for Mosquito-Borne Pathogen Modeling","text":"exDE software implements mathematical framework setting , analyzing, solving models mosquito-borne pathogen dynamics control systems ordinary delay differential equations. framework designed model spatial transmission dynamics pathogen within defined spatial domain; spatial ecology population dynamics mosquitoes within domain; exogenous forcing weather vector control; malaria mosquito importation. software also supports population dynamic models stratified human populations, including aging demographic changes. main focus software development malaria, framework capabilities model mosquito-transmitted pathogens. software aims fully modular: implements plug--play computation broad class simulation models describing dynamics control mosquito-transmitted pathogens. Modularity achieved combination methods: functions compute derivatives use method dispatches parameter lists component used compute full set differential equations; interfaces blood feeding egg laying biologically realistic rigidly defined guarantee mathematical consistency; large set additional features implemented careful attention detail guarantee consistency avoid conflicts. function exDE::xDE_diffeqn computes gradient state variables modular components can used excellent solvers deSolve, differential equation solvers R. exDE can regarded continuous-time companion discrete stochastic Micro-MoB framework. get started, please consider reading articles drop panels , website. 3 sections ending “Component” describe particular models implementing interface components (adult mosquitoes, aquatic mosquitoes, humans), show simulation equilibrium values. section “Articles” -depth examples, including extended walk set run model vignette(\"ex_534\"), guide contribute, example running model exDE external forcing model ITN (insecticide treated nets) based vector control vignette(\"vc_lemenach\"). section “Functions” documents function exported package.","code":""},{"path":"https://dd-harp.github.io/exDE/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Extensible Differential Equations for Mosquito-Borne Pathogen Modeling","text":"install latest version GitHub, run following lines code R session. Alternatively, can install directly CRAN (please aware version CRAN may latest version GitHub):","code":"library(devtools) devtools::install_github(\"dd-harp/exDE\") install.packages(\"exDE\")"},{"path":"https://dd-harp.github.io/exDE/index.html","id":"contributing","dir":"","previous_headings":"","what":"Contributing","title":"Extensible Differential Equations for Mosquito-Borne Pathogen Modeling","text":"information contribute development exDE, please read article contribute vignette(\"Contributing\")! questions, comments, bug reports, suggestions, first point contact development team GitHub Issues. specifically submitting bug report, please check bug reporting guide. interested collaborating extensive model development (e.g. new mosquito model), please hesitate contact authors, whose email addresses can found DESCRIPTION file. welcome issues encourage contribution regardless experience; length contributing guide intended intimidating, merely complete. responsibility package maintainers help new contributors understand conventions guide contributions successful conclusion.","code":""},{"path":"https://dd-harp.github.io/exDE/index.html","id":"model-building-in-exde","dir":"","previous_headings":"","what":"Model building in exDE","title":"Extensible Differential Equations for Mosquito-Borne Pathogen Modeling","text":"Models mosquito borne pathogen transmission systems naturally modular, structured vector life stage, host population strata, spatial locations (patches) transmission occurs (see figure ).  Models exDE framework constructed 3 dynamical components: ℳ: adult mosquitoes, whose dynamics described dℳ/dt ℒ: aquatic (immature) mosquitoes, whose dynamics described dℒ/dt 𝒳: human population, whose dynamics described d𝒳/dt combined state 3 components entire state dynamical model, combined dynamics described differential equations represents full endogenous dynamics system. addition 2 components directly contribute state model, instead modify parameters compute intermediate quantities represent external influences system. : Exogenous forcing: weather, climate, unmodeled populations Vector control: public health mosquito control interventions affect dynamical components also functions handle exchange information (flows) dynamical components couple dynamics. Bloodfeeding process adult mosquitoes seek feed blood hosts, results quantities EIR (entomological inoculation rate) κ, net infectiousness humans mosquitoes, couple dynamics ℳ 𝒳. Likewise emergence new adults aquatic habitats egg laying adults habitats couples ℳ ℒ. function exDE::xDE_diffeqn compute necessary quantities returns vector derivatives state variables can used solve trajectories model exDE. program flow within function summarized diagram:  information, please read research article describing theory behind model.","code":""},{"path":"https://dd-harp.github.io/exDE/index.html","id":"acknowledgements","dir":"","previous_headings":"","what":"Acknowledgements","title":"Extensible Differential Equations for Mosquito-Borne Pathogen Modeling","text":"Version 1.0 software designed Sean L. Wu Professor David L. Smith. code written Sean L. Wu. anticipate active development exDE MicroMoB add new models fill important needs. idea developing modular software simulate dynamics control mosquito-borne pathogens originated sometime around 2009 Emerging Pathogens Institute, University Florida. took much longer anticipated finish. concepts appeared various publications. algorithms trace back software packages never launched, someday might yet completed (e.g., MASH). retrospect, key challenge blood feeding, one. inception, project supported grants Bill Melinda Gates Foundation, including (recently) Modeling Adaptive Malaria Control (INV 030600, PI = David L Smith, University Washington). software part RAMP (Robust Analytics Malaria Policy), core analytical methodology developed support adaptive malaria control. RAMP project includes RAMP-UW team University Washington based Seattle Washington, RAMP-Uganda team based Kampala, Uganda, provides analytics support National Malaria Control Division, Ministry Health, Uganda. model features inspired discussions mosquito working groups (led Professor Thomas Scott) RAPIDD (Research Policy Infectious Disease Dynamics). time, project benefited unwavering support inspiration late F. Ellis McKenzie, Fogarty International Center. Development exDE supported, part, grant US National Institute Allergies Infectious Diseases (NIAID) fund project Spatial Targeting Adaptive Vector Control Residual Transmission Malaria Elimination Urban African Settings (R01 AI163398, PI = David L Smith), supported collaboration Bioko Island Malaria Elimination Program. Development software benefited funding collaboration NIAID grant Program Resistance, Immunology, Surveillance & Modeling Malaria Uganda (PRISM) (2U19AI089674, PIs = Grant Dorsey, University California San Francisco; Moses Kamya, Infectious Diseases Research Collaboration), part International Centers Excellence Malaria Research (ICEMR) program. Funding develop models West Nile Virus support Harris County Public Health funded NSF part project, Computing Biome (PI= Janos Sztipanovits). project part Convergence Accelerator program National Science Foundation, Directorate Technology, Innovation, Partnerships (TIP) (NSF 2040688 NSF 2040688, PI=Janos Sztipanovits, Vanderbilt University).","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up exogenous variables for abiotic forcing — Abiotic.forced","title":"Set up exogenous variables for abiotic forcing — Abiotic.forced","text":"Implements Abiotic abiotic forcing","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up exogenous variables for abiotic forcing — Abiotic.forced","text":"","code":"# S3 method for forced Abiotic(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up exogenous variables for abiotic forcing — Abiotic.forced","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up exogenous variables for abiotic forcing — Abiotic.forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up exogenous variables for abiotic forcing — Abiotic","title":"Set up exogenous variables for abiotic forcing — Abiotic","text":"method dispatches type pars$ABIOTIC.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up exogenous variables for abiotic forcing — Abiotic","text":"","code":"Abiotic(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up exogenous variables for abiotic forcing — Abiotic","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up exogenous variables for abiotic forcing — Abiotic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up exogenous variables for abiotic forcing — Abiotic.null","title":"Set up exogenous variables for abiotic forcing — Abiotic.null","text":"Implements Abiotic null model exogenous forcing (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up exogenous variables for abiotic forcing — Abiotic.null","text":"","code":"# S3 method for null Abiotic(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up exogenous variables for abiotic forcing — Abiotic.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up exogenous variables for abiotic forcing — Abiotic.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSpray.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for mass spraying — AreaSpray","title":"Methods for mass spraying — AreaSpray","text":"method dispatches type pars$AREA_SPRAY.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSpray.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for mass spraying — AreaSpray","text":"","code":"AreaSpray(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AreaSpray.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for mass spraying — AreaSpray","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSpray.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for mass spraying — AreaSpray","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSpray.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up mass spraying — AreaSpray.null","title":"Set up mass spraying — AreaSpray.null","text":"Implements AreaSpray null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSpray.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up mass spraying — AreaSpray.null","text":"","code":"# S3 method for null AreaSpray(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AreaSpray.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up mass spraying — AreaSpray.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSpray.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up mass spraying — AreaSpray.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffectSizes.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for mass spraying — AreaSprayEffectSizes","title":"Methods for mass spraying — AreaSprayEffectSizes","text":"method dispatches type pars$AREA_SPRAY.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffectSizes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for mass spraying — AreaSprayEffectSizes","text":"","code":"AreaSprayEffectSizes(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffectSizes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for mass spraying — AreaSprayEffectSizes","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffectSizes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for mass spraying — AreaSprayEffectSizes","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffectSizes.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up mass spraying — AreaSprayEffectSizes.null","title":"Set up mass spraying — AreaSprayEffectSizes.null","text":"Implements AreaSprayEffectSizes null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffectSizes.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up mass spraying — AreaSprayEffectSizes.null","text":"","code":"# S3 method for null AreaSprayEffectSizes(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffectSizes.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up mass spraying — AreaSprayEffectSizes.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffectSizes.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up mass spraying — AreaSprayEffectSizes.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffects.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for mass spraying — AreaSprayEffects","title":"Methods for mass spraying — AreaSprayEffects","text":"method dispatches type pars$AREA_SPRAY.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for mass spraying — AreaSprayEffects","text":"","code":"AreaSprayEffects(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for mass spraying — AreaSprayEffects","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for mass spraying — AreaSprayEffects","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffects.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up mass spraying — AreaSprayEffects.null","title":"Set up mass spraying — AreaSprayEffects.null","text":"Implements AreaSprayEffects null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffects.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up mass spraying — AreaSprayEffects.null","text":"","code":"# S3 method for null AreaSprayEffects(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffects.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up mass spraying — AreaSprayEffects.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffects.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up mass spraying — AreaSprayEffects.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute availability of local humans for blood feeding — AvailableBlood.forced","title":"Compute availability of local humans for blood feeding — AvailableBlood.forced","text":"Compute availability pathogen's hosts blood feeding","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute availability of local humans for blood feeding — AvailableBlood.forced","text":"","code":"# S3 method for forced AvailableBlood(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute availability of local humans for blood feeding — AvailableBlood.forced","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute availability of local humans for blood feeding — AvailableBlood.forced","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.html","id":null,"dir":"Reference","previous_headings":"","what":"Update the availability of blood hosts — AvailableBlood","title":"Update the availability of blood hosts — AvailableBlood","text":"method dispatches type pars$BFpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update the availability of blood hosts — AvailableBlood","text":"","code":"AvailableBlood(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update the availability of blood hosts — AvailableBlood","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update the availability of blood hosts — AvailableBlood","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.setup.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute availability of local humans for blood feeding — AvailableBlood.setup","title":"Compute availability of local humans for blood feeding — AvailableBlood.setup","text":"Compute availability pathogen's hosts blood feeding","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.setup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute availability of local humans for blood feeding — AvailableBlood.setup","text":"","code":"# S3 method for setup AvailableBlood(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.setup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute availability of local humans for blood feeding — AvailableBlood.setup","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.setup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute availability of local humans for blood feeding — AvailableBlood.setup","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute availability of local humans for blood feeding — AvailableBlood.static","title":"Compute availability of local humans for blood feeding — AvailableBlood.static","text":"Compute availability pathogen's hosts blood feeding","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute availability of local humans for blood feeding — AvailableBlood.static","text":"","code":"# S3 method for static AvailableBlood(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute availability of local humans for blood feeding — AvailableBlood.static","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute availability of local humans for blood feeding — AvailableBlood.static","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute total availability of aquatic habitats — AvailableHabitat.forced","title":"Compute total availability of aquatic habitats — AvailableHabitat.forced","text":"Computes availability aquatic habitats","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute total availability of aquatic habitats — AvailableHabitat.forced","text":"","code":"# S3 method for forced AvailableHabitat(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute total availability of aquatic habitats — AvailableHabitat.forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute total availability of aquatic habitats — AvailableHabitat.forced","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.html","id":null,"dir":"Reference","previous_headings":"","what":"Update the availability of aquatic habitats — AvailableHabitat","title":"Update the availability of aquatic habitats — AvailableHabitat","text":"method dispatches type pars$EGGpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update the availability of aquatic habitats — AvailableHabitat","text":"","code":"AvailableHabitat(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update the availability of aquatic habitats — AvailableHabitat","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update the availability of aquatic habitats — AvailableHabitat","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.simple.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute total availability of aquatic habitats — AvailableHabitat.simple","title":"Compute total availability of aquatic habitats — AvailableHabitat.simple","text":"Computes availability aquatic habitats static model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.simple.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute total availability of aquatic habitats — AvailableHabitat.simple","text":"","code":"# S3 method for simple AvailableHabitat(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.simple.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute total availability of aquatic habitats — AvailableHabitat.simple","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.simple.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute total availability of aquatic habitats — AvailableHabitat.simple","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute total availability of aquatic habitats — AvailableHabitat.static","title":"Compute total availability of aquatic habitats — AvailableHabitat.static","text":"Computes availability aquatic habitats static model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute total availability of aquatic habitats — AvailableHabitat.static","text":"","code":"# S3 method for static AvailableHabitat(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute total availability of aquatic habitats — AvailableHabitat.static","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute total availability of aquatic habitats — AvailableHabitat.static","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute total availability of sugar — AvailableSugar.forced","title":"Compute total availability of sugar — AvailableSugar.forced","text":"Computes availability sugar","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute total availability of sugar — AvailableSugar.forced","text":"","code":"# S3 method for forced AvailableSugar(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute total availability of sugar — AvailableSugar.forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute total availability of sugar — AvailableSugar.forced","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.html","id":null,"dir":"Reference","previous_headings":"","what":"Update the availability of sugar — AvailableSugar","title":"Update the availability of sugar — AvailableSugar","text":"method dispatches type pars$SUGAR.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update the availability of sugar — AvailableSugar","text":"","code":"AvailableSugar(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update the availability of sugar — AvailableSugar","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update the availability of sugar — AvailableSugar","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute total availability of sugar — AvailableSugar.static","title":"Compute total availability of sugar — AvailableSugar.static","text":"Computes availability sugar static model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute total availability of sugar — AvailableSugar.static","text":"","code":"# S3 method for static AvailableSugar(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute total availability of sugar — AvailableSugar.static","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute total availability of sugar — AvailableSugar.static","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify baseline bionomic parameters, called from VectorControlEffectSizes — BedNetEffectSizes","title":"Modify baseline bionomic parameters, called from VectorControlEffectSizes — BedNetEffectSizes","text":"method dispatches type pars$ITNefsz.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify baseline bionomic parameters, called from VectorControlEffectSizes — BedNetEffectSizes","text":"","code":"BedNetEffectSizes(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify baseline bionomic parameters, called from VectorControlEffectSizes — BedNetEffectSizes","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify baseline bionomic parameters, called from VectorControlEffectSizes — BedNetEffectSizes","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.lemenach.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify baseline values due to vector control — BedNetEffectSizes.lemenach","title":"Modify baseline values due to vector control — BedNetEffectSizes.lemenach","text":"Implements BedNetEffectSizes Le Menach ITN model vector control","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.lemenach.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify baseline values due to vector control — BedNetEffectSizes.lemenach","text":"","code":"# S3 method for lemenach BedNetEffectSizes(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.lemenach.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify baseline values due to vector control — BedNetEffectSizes.lemenach","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.lemenach.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify baseline values due to vector control — BedNetEffectSizes.lemenach","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Bed net ownership — BedNetEffectSizes.null","title":"Bed net ownership — BedNetEffectSizes.null","text":"Implements BedNetEffectSizes null model bed nets (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bed net ownership — BedNetEffectSizes.null","text":"","code":"# S3 method for null BedNetEffectSizes(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bed net ownership — BedNetEffectSizes.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bed net ownership — BedNetEffectSizes.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffects.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify variables or parameters, called from VectorControlEffects — BedNetEffects","title":"Modify variables or parameters, called from VectorControlEffects — BedNetEffects","text":"method dispatches type pars$ITNeff.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify variables or parameters, called from VectorControlEffects — BedNetEffects","text":"","code":"BedNetEffects(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify variables or parameters, called from VectorControlEffects — BedNetEffects","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify variables or parameters, called from VectorControlEffects — BedNetEffects","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffects.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Bed net ownership — BedNetEffects.null","title":"Bed net ownership — BedNetEffects.null","text":"Implements BedNetEffects null model bed nets (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffects.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bed net ownership — BedNetEffects.null","text":"","code":"# S3 method for null BedNetEffects(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffects.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bed net ownership — BedNetEffects.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffects.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bed net ownership — BedNetEffects.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for dynamic human and mosquito behaviors — Behavior.forced","title":"Methods for dynamic human and mosquito behaviors — Behavior.forced","text":"Implements Behavior forced model (changes)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for dynamic human and mosquito behaviors — Behavior.forced","text":"","code":"# S3 method for forced Behavior(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for dynamic human and mosquito behaviors — Behavior.forced","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for dynamic human and mosquito behaviors — Behavior.forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for dynamic human and mosquito behaviors — Behavior","title":"Methods for dynamic human and mosquito behaviors — Behavior","text":"method dispatches type pars$BEHAVIOR.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for dynamic human and mosquito behaviors — Behavior","text":"","code":"Behavior(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for dynamic human and mosquito behaviors — Behavior","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for dynamic human and mosquito behaviors — Behavior","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for dynamic human and mosquito behaviors — Behavior.null","title":"Methods for dynamic human and mosquito behaviors — Behavior.null","text":"Implements Behavior null model (changes)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for dynamic human and mosquito behaviors — Behavior.null","text":"","code":"# S3 method for null Behavior(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for dynamic human and mosquito behaviors — Behavior.null","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for dynamic human and mosquito behaviors — Behavior.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.Ldynamic.html","id":null,"dir":"Reference","previous_headings":"","what":"Set bionomic parameter rates relative to baseline — Bionomics.Ldynamic","title":"Set bionomic parameter rates relative to baseline — Bionomics.Ldynamic","text":"calls Lbionomics species time step","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.Ldynamic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set bionomic parameter rates relative to baseline — Bionomics.Ldynamic","text":"","code":"# S3 method for Ldynamic Bionomics(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.Ldynamic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set bionomic parameter rates relative to baseline — Bionomics.Ldynamic","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.Ldynamic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set bionomic parameter rates relative to baseline — Bionomics.Ldynamic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.Mdynamic.html","id":null,"dir":"Reference","previous_headings":"","what":"Set bionomic parameter rates relative to baseline — Bionomics.Mdynamic","title":"Set bionomic parameter rates relative to baseline — Bionomics.Mdynamic","text":"calls Mbionomics Lbionmics species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.Mdynamic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set bionomic parameter rates relative to baseline — Bionomics.Mdynamic","text":"","code":"# S3 method for Mdynamic Bionomics(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.Mdynamic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set bionomic parameter rates relative to baseline — Bionomics.Mdynamic","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.Mdynamic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set bionomic parameter rates relative to baseline — Bionomics.Mdynamic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.dynamic.html","id":null,"dir":"Reference","previous_headings":"","what":"Set bionomic parameter rates relative to baseline — Bionomics.dynamic","title":"Set bionomic parameter rates relative to baseline — Bionomics.dynamic","text":"calls Mbionomics Lbionmics species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.dynamic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set bionomic parameter rates relative to baseline — Bionomics.dynamic","text":"","code":"# S3 method for dynamic Bionomics(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.dynamic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set bionomic parameter rates relative to baseline — Bionomics.dynamic","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.dynamic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set bionomic parameter rates relative to baseline — Bionomics.dynamic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.html","id":null,"dir":"Reference","previous_headings":"","what":"Set bionomic parameter rates relative to baseline — Bionomics","title":"Set bionomic parameter rates relative to baseline — Bionomics","text":"calls Mbionomics Lbionmics species. function resets bionomic parameters pre-control baseline value, can later modified vector control. models, pre-control baseline computed function resource availability.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set bionomic parameter rates relative to baseline — Bionomics","text":"","code":"Bionomics(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set bionomic parameter rates relative to baseline — Bionomics","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set bionomic parameter rates relative to baseline — Bionomics","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.setup.html","id":null,"dir":"Reference","previous_headings":"","what":"Set bionomic parameter rates relative to baseline — Bionomics.setup","title":"Set bionomic parameter rates relative to baseline — Bionomics.setup","text":"calls Mbionomics Lbionmics species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.setup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set bionomic parameter rates relative to baseline — Bionomics.setup","text":"","code":"# S3 method for setup Bionomics(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.setup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set bionomic parameter rates relative to baseline — Bionomics.setup","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.setup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set bionomic parameter rates relative to baseline — Bionomics.setup","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Set bionomic parameter rates relative to baseline — Bionomics.static","title":"Set bionomic parameter rates relative to baseline — Bionomics.static","text":"calls Mbionomics Lbionmics species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set bionomic parameter rates relative to baseline — Bionomics.static","text":"","code":"# S3 method for static Bionomics(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set bionomic parameter rates relative to baseline — Bionomics.static","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set bionomic parameter rates relative to baseline — Bionomics.static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Births.html","id":null,"dir":"Reference","previous_headings":"","what":"A function that computes the birth rate for human populations — Births","title":"A function that computes the birth rate for human populations — Births","text":"method dispatches type pars$Hpar$Births","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Births.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function that computes the birth rate for human populations — Births","text":"","code":"Births(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/Births.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function that computes the birth rate for human populations — Births","text":"t current simulation time y state vector pars list index host species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Births.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function that computes the birth rate for human populations — Births","text":"see help pages specific methods","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Births.zero.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives of demographic changes in human populations — Births.zero","title":"Derivatives of demographic changes in human populations — Births.zero","text":"Implements Births static population models","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Births.zero.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives of demographic changes in human populations — Births.zero","text":"","code":"# S3 method for zero Births(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/Births.zero.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives of demographic changes in human populations — Births.zero","text":"t current simulation time y state vector pars list index host species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Births.zero.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives of demographic changes in human populations — Births.zero","text":"numeric vector zeros","code":""},{"path":"https://dd-harp.github.io/exDE/reference/CareSeeking.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of exogenous variables describing care seeking — CareSeeking","title":"Set the values of exogenous variables describing care seeking — CareSeeking","text":"method dispatches type pars$CARE_SEEKING.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/CareSeeking.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of exogenous variables describing care seeking — CareSeeking","text":"","code":"CareSeeking(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/CareSeeking.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of exogenous variables describing care seeking — CareSeeking","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/CareSeeking.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of exogenous variables describing care seeking — CareSeeking","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/CareSeeking.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of exogenous variables describing care seeking — CareSeeking.null","title":"Set the values of exogenous variables describing care seeking — CareSeeking.null","text":"Implements CareSeeking null model care seeking (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/CareSeeking.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of exogenous variables describing care seeking — CareSeeking.null","text":"","code":"# S3 method for null CareSeeking(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/CareSeeking.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of exogenous variables describing care seeking — CareSeeking.null","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/CareSeeking.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of exogenous variables describing care seeking — CareSeeking.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up exogenous variables for civil forcing — Civil.forced","title":"Set up exogenous variables for civil forcing — Civil.forced","text":"Implements Civil civil forcing","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up exogenous variables for civil forcing — Civil.forced","text":"","code":"# S3 method for forced Civil(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Civil.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up exogenous variables for civil forcing — Civil.forced","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up exogenous variables for civil forcing — Civil.forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up exogenous variables for civil forcing — Civil","title":"Set up exogenous variables for civil forcing — Civil","text":"method dispatches type pars$CIVIL.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up exogenous variables for civil forcing — Civil","text":"","code":"Civil(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Civil.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up exogenous variables for civil forcing — Civil","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up exogenous variables for civil forcing — Civil","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up exogenous variables for civil forcing — Civil.null","title":"Set up exogenous variables for civil forcing — Civil.null","text":"Implements Civil null model exogenous forcing (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up exogenous variables for civil forcing — Civil.null","text":"","code":"# S3 method for null Civil(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Civil.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up exogenous variables for civil forcing — Civil.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up exogenous variables for civil forcing — Civil.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Clinic.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for distributing interventions during clinical visits — Clinic","title":"Methods for distributing interventions during clinical visits — Clinic","text":"method dispatches type pars$CLINIC.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Clinic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for distributing interventions during clinical visits — Clinic","text":"","code":"Clinic(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Clinic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for distributing interventions during clinical visits — Clinic","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Clinic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for distributing interventions during clinical visits — Clinic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Clinic.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for distributing interventions during clinical visits — Clinic.null","title":"Methods for distributing interventions during clinical visits — Clinic.null","text":"Implements Clinic null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Clinic.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for distributing interventions during clinical visits — Clinic.null","text":"","code":"# S3 method for null Clinic(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Clinic.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for distributing interventions during clinical visits — Clinic.null","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Clinic.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for distributing interventions during clinical visits — Clinic.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify parameters due to exogenous forcing by all kinds of control — Control.forced","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.forced","text":"Implements Control model control","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.forced","text":"","code":"# S3 method for forced Control(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Control.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.forced","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify parameters due to exogenous forcing by all kinds of control — Control","title":"Modify parameters due to exogenous forcing by all kinds of control — Control","text":"method dispatches type pars$CONTROL.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify parameters due to exogenous forcing by all kinds of control — Control","text":"","code":"Control(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify parameters due to exogenous forcing by all kinds of control — Control","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify parameters due to exogenous forcing by all kinds of control — Control","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify parameters due to exogenous forcing by all kinds of control — Control.null","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.null","text":"Implements Control null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.null","text":"","code":"# S3 method for null Control(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Control.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.null","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify parameters due to exogenous forcing by all kinds of control — Control.static","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.static","text":"Implements Control static model; setting , nothing","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.static","text":"","code":"# S3 method for static Control(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Control.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.static","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Development.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up developments — Development","title":"Set up developments — Development","text":"method dispatches type pars$DEVELOPMENT.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Development.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up developments — Development","text":"","code":"Development(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Development.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up developments — Development","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Development.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up developments — Development","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Development.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up developments — Development.null","title":"Set up developments — Development.null","text":"Implements Development null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Development.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up developments — Development.null","text":"","code":"# S3 method for null Development(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Development.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up developments — Development.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Development.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up developments — Development.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/DistributeBedNets.html","id":null,"dir":"Reference","previous_headings":"","what":"Distribute bed nets, called from Control(VectorControl) — DistributeBedNets","title":"Distribute bed nets, called from Control(VectorControl) — DistributeBedNets","text":"method dispatches type pars$ITNdist.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/DistributeBedNets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Distribute bed nets, called from Control(VectorControl) — DistributeBedNets","text":"","code":"DistributeBedNets(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/DistributeBedNets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Distribute bed nets, called from Control(VectorControl) — DistributeBedNets","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/DistributeBedNets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Distribute bed nets, called from Control(VectorControl) — DistributeBedNets","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/DistributeBedNets.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Distribute bed nets — DistributeBedNets.null","title":"Distribute bed nets — DistributeBedNets.null","text":"Implements DistributeBedNets null model bed nets (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/DistributeBedNets.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Distribute bed nets — DistributeBedNets.null","text":"","code":"# S3 method for null DistributeBedNets(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/DistributeBedNets.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Distribute bed nets — DistributeBedNets.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/DistributeBedNets.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Distribute bed nets — DistributeBedNets.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the EIP — EIP","title":"Compute the EIP — EIP","text":"method dispatches type EIPmod.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the EIP — EIP","text":"","code":"EIP(t, EIPmod)"},{"path":"https://dd-harp.github.io/exDE/reference/EIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the EIP — EIP","text":"t current simulation time EIPmod list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the EIP — EIP","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EIP.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify parameters due to exogenous forcing by all kinds of control — EIP.static","title":"Modify parameters due to exogenous forcing by all kinds of control — EIP.static","text":"Implements EIP static model (EIP constant)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EIP.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify parameters due to exogenous forcing by all kinds of control — EIP.static","text":"","code":"# S3 method for static EIP(t, EIPmod)"},{"path":"https://dd-harp.github.io/exDE/reference/EIP.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify parameters due to exogenous forcing by all kinds of control — EIP.static","text":"t current simulation time EIPmod list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EIP.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify parameters due to exogenous forcing by all kinds of control — EIP.static","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.dynamic.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute eggs laid — EggLaying.dynamic","title":"Compute eggs laid — EggLaying.dynamic","text":"Computes eggs laid s^th species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.dynamic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute eggs laid — EggLaying.dynamic","text":"","code":"# S3 method for dynamic EggLaying(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.dynamic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute eggs laid — EggLaying.dynamic","text":"t time y state variables pars model object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.dynamic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute eggs laid — EggLaying.dynamic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute eggs laid — EggLaying","title":"Compute eggs laid — EggLaying","text":"Computes eggs laid s^th species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute eggs laid — EggLaying","text":"","code":"EggLaying(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute eggs laid — EggLaying","text":"t time y state variables pars model object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute eggs laid — EggLaying","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.setup.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute eggs laid — EggLaying.setup","title":"Compute eggs laid — EggLaying.setup","text":"Computes eggs laid s^th species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.setup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute eggs laid — EggLaying.setup","text":"","code":"# S3 method for setup EggLaying(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.setup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute eggs laid — EggLaying.setup","text":"t time y state variables pars model object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.setup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute eggs laid — 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Dynamics and Searching — HabitatDynamics","text":"Set values habitat search weights exogenous variables describing habitat_dynamics. method dispatches type pars$HABITAT_DYNAMICS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HabitatDynamics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Habitat Dynamics and Searching — HabitatDynamics","text":"","code":"HabitatDynamics(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/HabitatDynamics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Habitat Dynamics and Searching — HabitatDynamics","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HabitatDynamics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Habitat Dynamics and Searching — 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pars$HYDROLOGY.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Hydrology.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of exogenous variables describing hydrology — Hydrology","text":"","code":"Hydrology(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Hydrology.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of exogenous variables describing hydrology — Hydrology","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Hydrology.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of exogenous variables describing hydrology — Hydrology","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Hydrology.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of exogenous variables describing hydrology — 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bionomic parameters to baseline — MBionomics.basicM","title":"Set bionomic parameters to baseline — MBionomics.basicM","text":"Implements MBionomics basicM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set bionomic parameters to baseline — MBionomics.basicM","text":"","code":"# S3 method for basicM MBionomics(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set bionomic parameters to baseline — MBionomics.basicM","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set bionomic parameters to baseline — MBionomics.basicM","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.html","id":null,"dir":"Reference","previous_headings":"","what":"Set bloodfeeding and mortality rates to baseline — MBionomics","title":"Set bloodfeeding and mortality rates to baseline — MBionomics","text":"method dispatches type pars$MYZpar. set values bionomic parameters baseline values.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set bloodfeeding and mortality rates to baseline — MBionomics","text":"","code":"MBionomics(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set bloodfeeding and mortality rates to baseline — MBionomics","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set bloodfeeding and mortality rates to baseline — MBionomics","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for mass medical — MassMedical.forced","title":"Methods for mass medical — MassMedical.forced","text":"Implements MassMedical","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for mass medical — MassMedical.forced","text":"","code":"# S3 method for forced MassMedical(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for mass medical — MassMedical.forced","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for mass medical — MassMedical.forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for mass medical interventions — MassMedical","title":"Methods for mass medical interventions — MassMedical","text":"method dispatches type pars$MASS_MED.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for mass medical interventions — MassMedical","text":"","code":"MassMedical(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for mass medical interventions — MassMedical","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for mass medical interventions — MassMedical","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for mass medical — MassMedical.null","title":"Methods for mass medical — MassMedical.null","text":"Implements MassMedical null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for mass medical — MassMedical.null","text":"","code":"# S3 method for null MassMedical(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for mass medical — MassMedical.null","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for mass medical — MassMedical.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OtherBloodHosts.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts","title":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts","text":"method dispatches type pars$OTHER_BLOOD.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OtherBloodHosts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts","text":"","code":"OtherBloodHosts(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/OtherBloodHosts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OtherBloodHosts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OtherBloodHosts.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts.static","title":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts.static","text":"Implements OtherBloodHosts static model other_blood_hosts (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OtherBloodHosts.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts.static","text":"","code":"# S3 method for static OtherBloodHosts(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/OtherBloodHosts.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts.static","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OtherBloodHosts.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts.static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OviTraps.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for oviposition traps — OviTraps","title":"Methods for oviposition traps — OviTraps","text":"method dispatches type pars$OVITRAPS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OviTraps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for oviposition traps — OviTraps","text":"","code":"OviTraps(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/OviTraps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for oviposition traps — OviTraps","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OviTraps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for oviposition traps — OviTraps","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OviTraps.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for oviposition traps — OviTraps.null","title":"Methods for oviposition traps — OviTraps.null","text":"Implements OviTraps null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OviTraps.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for oviposition traps — OviTraps.null","text":"","code":"# S3 method for null OviTraps(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/OviTraps.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for oviposition traps — OviTraps.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OviTraps.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for oviposition traps — OviTraps.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OwnBedNet.html","id":null,"dir":"Reference","previous_headings":"","what":"Model bed net loss, called from Control(VectorControl) — OwnBedNet","title":"Model bed net loss, called from Control(VectorControl) — OwnBedNet","text":"method dispatches type pars$ITNown.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OwnBedNet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Model bed net loss, called from Control(VectorControl) — OwnBedNet","text":"","code":"OwnBedNet(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/OwnBedNet.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Model bed net loss, called from Control(VectorControl) — OwnBedNet","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OwnBedNet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Model bed net loss, called from Control(VectorControl) — OwnBedNet","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OwnBedNet.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Bed net ownership — OwnBedNet.null","title":"Bed net ownership — OwnBedNet.null","text":"Implements OwnBedNet null model bed nets (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OwnBedNet.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bed net ownership — OwnBedNet.null","text":"","code":"# S3 method for null OwnBedNet(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/OwnBedNet.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bed net ownership — OwnBedNet.null","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OwnBedNet.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bed net ownership — OwnBedNet.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Rainfall.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing rainfall — Rainfall","title":"Methods for exogenous variables describing rainfall — Rainfall","text":"method dispatches type pars$RAINFALL.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Rainfall.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing rainfall — Rainfall","text":"","code":"Rainfall(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Rainfall.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing rainfall — Rainfall","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Rainfall.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing rainfall — Rainfall","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Rainfall.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing rainfall — Rainfall.null","title":"Methods for exogenous variables describing rainfall — Rainfall.null","text":"Implements Rainfall null model (variables)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Rainfall.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing rainfall — Rainfall.null","text":"","code":"# S3 method for null Rainfall(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Rainfall.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing rainfall — Rainfall.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Rainfall.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing rainfall — Rainfall.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Relative_Humidity.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing relative humidity — Relative_Humidity","title":"Methods for exogenous variables describing relative humidity — Relative_Humidity","text":"method dispatches type pars$HUMIDITY.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Relative_Humidity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing relative humidity — Relative_Humidity","text":"","code":"Relative_Humidity(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Relative_Humidity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing relative humidity — Relative_Humidity","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Relative_Humidity.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing relative humidity — Relative_Humidity","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Relative_Humidity.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing relative humidity — Relative_Humidity.null","title":"Methods for exogenous variables describing relative humidity — Relative_Humidity.null","text":"Implements Relative_Humidity null model (variables)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Relative_Humidity.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing relative humidity — Relative_Humidity.null","text":"","code":"# S3 method for null Relative_Humidity(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Relative_Humidity.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing relative humidity — Relative_Humidity.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Relative_Humidity.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing relative humidity — Relative_Humidity.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for resources — Resources.forced","title":"Methods for resources — Resources.forced","text":"Implements Resources","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for resources — Resources.forced","text":"","code":"# S3 method for forced Resources(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Resources.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for resources — Resources.forced","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for resources — Resources.forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of exogenous variables describing available mosquito resources — Resources","title":"Set the values of exogenous variables describing available mosquito resources — Resources","text":"method dispatches type pars$RESOURCES.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of exogenous variables describing available mosquito resources — Resources","text":"","code":"Resources(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Resources.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of exogenous variables describing available mosquito resources — Resources","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of exogenous variables describing available mosquito resources — Resources","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.setup.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify resources and resource availability — Resources.setup","title":"Modify resources and resource availability — Resources.setup","text":"Implements Resources null model resources","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.setup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify resources and resource availability — Resources.setup","text":"","code":"# S3 method for setup Resources(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Resources.setup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify resources and resource availability — Resources.setup","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.setup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify resources and resource availability — Resources.setup","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify resources and resource availability — Resources.static","title":"Modify resources and resource availability — Resources.static","text":"Implements Resources null model resources","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify resources and resource availability — Resources.static","text":"","code":"# S3 method for static Resources(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Resources.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify resources and resource availability — Resources.static","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify resources and resource availability — Resources.static","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Shock.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up shocks — Shock","title":"Set up shocks — Shock","text":"method dispatches type pars$SHOCK.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Shock.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up shocks — Shock","text":"","code":"Shock(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Shock.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up shocks — Shock","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Shock.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up shocks — Shock","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Shock.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up shocks — Shock.null","title":"Set up shocks — Shock.null","text":"Implements Shock null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Shock.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up shocks — Shock.null","text":"","code":"# S3 method for null Shock(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Shock.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up shocks — Shock.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Shock.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up shocks — Shock.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SprayHouses.html","id":null,"dir":"Reference","previous_headings":"","what":"Do mass house spraying (IRS) — SprayHouses","title":"Do mass house spraying (IRS) — SprayHouses","text":"method dispatches type pars$IRS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SprayHouses.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Do mass house spraying (IRS) — SprayHouses","text":"","code":"SprayHouses(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SprayHouses.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Do mass house spraying (IRS) — SprayHouses","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SprayHouses.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Do mass house spraying (IRS) — SprayHouses","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SprayHouses.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Do mass house spraying (IRS) — SprayHouses.null","title":"Do mass house spraying (IRS) — SprayHouses.null","text":"method dispatches type pars$IRS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SprayHouses.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Do mass house spraying (IRS) — SprayHouses.null","text":"","code":"# S3 method for null SprayHouses(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SprayHouses.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Do mass house spraying (IRS) — SprayHouses.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SprayHouses.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Do mass house spraying (IRS) — SprayHouses.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffectSizes.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes","title":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes","text":"method dispatches type pars$SUGAR_BAITS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffectSizes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes","text":"","code":"SugarBaitEffectSizes(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffectSizes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffectSizes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffectSizes.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes.null","title":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes.null","text":"method dispatches type pars$SUGAR_BAITS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffectSizes.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes.null","text":"","code":"# S3 method for null SugarBaitEffectSizes(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffectSizes.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes.null","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffectSizes.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffects.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for the durability and effects of the sugar baits — SugarBaitEffects","title":"Methods for the durability and effects of the sugar baits — SugarBaitEffects","text":"method dispatches type pars$SUGAR_BAITS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for the durability and effects of the sugar baits — SugarBaitEffects","text":"","code":"SugarBaitEffects(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for the durability and effects of the sugar baits — SugarBaitEffects","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for the durability and effects of the sugar baits — SugarBaitEffects","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffects.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for the effects of the sugar baits — SugarBaitEffects.null","title":"Methods for the effects of the sugar baits — SugarBaitEffects.null","text":"Implements SugarBaitEffects null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffects.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for the effects of the sugar baits — SugarBaitEffects.null","text":"","code":"# S3 method for null SugarBaitEffects(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffects.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for the effects of the sugar baits — SugarBaitEffects.null","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffects.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for the effects of the sugar baits — SugarBaitEffects.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaits.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for distributing sugar baits — SugarBaits","title":"Methods for distributing sugar baits — SugarBaits","text":"method dispatches type pars$SUGAR_BAITS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for distributing sugar baits — SugarBaits","text":"","code":"SugarBaits(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for distributing sugar baits — SugarBaits","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaits.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for distributing sugar baits — SugarBaits","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaits.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for sugar baits — SugarBaits.null","title":"Methods for sugar baits — SugarBaits.null","text":"Implements SugarBaits null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaits.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for sugar baits — SugarBaits.null","text":"","code":"# S3 method for null SugarBaits(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaits.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for sugar baits — SugarBaits.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaits.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for sugar baits — SugarBaits.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarDynamics.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of exogenous variables describing sugar — SugarDynamics","title":"Set the values of exogenous variables describing sugar — SugarDynamics","text":"method dispatches type pars$SUGAR.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarDynamics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of exogenous variables describing sugar — SugarDynamics","text":"","code":"SugarDynamics(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SugarDynamics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of exogenous variables describing sugar — SugarDynamics","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarDynamics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of exogenous variables describing sugar — SugarDynamics","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarDynamics.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of exogenous variables describing sugar — SugarDynamics.static","title":"Set the values of exogenous variables describing sugar — SugarDynamics.static","text":"Implements SugarDynamics static model sugar (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarDynamics.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of exogenous variables describing sugar — SugarDynamics.static","text":"","code":"# S3 method for static SugarDynamics(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SugarDynamics.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of exogenous variables describing sugar — SugarDynamics.static","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarDynamics.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of exogenous variables describing sugar — SugarDynamics.static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Temperature.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing temperature — Temperature","title":"Methods for exogenous variables describing temperature — Temperature","text":"method dispatches type pars$TEMPERATURE.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Temperature.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing temperature — Temperature","text":"","code":"Temperature(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Temperature.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing temperature — Temperature","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Temperature.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing temperature — Temperature","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Temperature.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing temperature — Temperature.null","title":"Methods for exogenous variables describing temperature — Temperature.null","text":"Implements Temperature null model (variables)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Temperature.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing temperature — Temperature.null","text":"","code":"# S3 method for null Temperature(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Temperature.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing temperature — Temperature.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Temperature.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing temperature — Temperature.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.dynamic.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute transmission terms, the dynamic case — Transmission.dynamic","title":"Compute transmission terms, the dynamic case — Transmission.dynamic","text":"method dispatches type pars$BFpar","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.dynamic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute transmission terms, the dynamic case — Transmission.dynamic","text":"","code":"# S3 method for dynamic Transmission(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.dynamic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute transmission terms, the dynamic case — Transmission.dynamic","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.dynamic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute transmission terms, the dynamic case — Transmission.dynamic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute transmission terms dynamically — Transmission","title":"Compute transmission terms dynamically — Transmission","text":"method dispatches type pars$BFpar","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute transmission terms dynamically — Transmission","text":"","code":"Transmission(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute transmission terms dynamically — Transmission","text":"t current simulation time y state vector pars, list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute transmission terms dynamically — Transmission","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.setup.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute transmission terms, the dynamic case — Transmission.setup","title":"Compute transmission terms, the dynamic case — Transmission.setup","text":"method dispatches type pars$BFpar","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.setup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute transmission terms, the dynamic case — Transmission.setup","text":"","code":"# S3 method for setup Transmission(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.setup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute transmission terms, the dynamic case — Transmission.setup","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.setup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute transmission terms, the dynamic case — Transmission.setup","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute transmission terms dynamically, no update required — Transmission.static","title":"Compute transmission terms dynamically, no update required — Transmission.static","text":"method dispatches type pars$BFpar","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute transmission terms dynamically, no update required — Transmission.static","text":"","code":"# S3 method for static Transmission(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute transmission terms dynamically, no update required — Transmission.static","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute transmission terms dynamically, no update required — Transmission.static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/TreatHabitats.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify values due to treat habitats as part of LSM,\ncalled by Control->VectorControl — TreatHabitats","title":"Modify values due to treat habitats as part of LSM,\ncalled by Control->VectorControl — TreatHabitats","text":"method dispatches type pars$LSM.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/TreatHabitats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify values due to treat habitats as part of LSM,\ncalled by Control->VectorControl — TreatHabitats","text":"","code":"TreatHabitats(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/TreatHabitats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify values due to treat habitats as part of LSM,\ncalled by Control->VectorControl — TreatHabitats","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/TreatHabitats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify values due to treat habitats as part of LSM,\ncalled by Control->VectorControl — TreatHabitats","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/TreatHabitats.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the null model for LSM — TreatHabitats.null","title":"Set up the null model for LSM — TreatHabitats.null","text":"method dispatches type pars$LSM","code":""},{"path":"https://dd-harp.github.io/exDE/reference/TreatHabitats.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the null model for LSM — TreatHabitats.null","text":"","code":"# S3 method for null TreatHabitats(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/TreatHabitats.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the null model for LSM — TreatHabitats.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/TreatHabitats.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the null model for LSM — TreatHabitats.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/UseBedNet.html","id":null,"dir":"Reference","previous_headings":"","what":"Model bed net usage, called from Behavior — UseBedNet","title":"Model bed net usage, called from Behavior — UseBedNet","text":"method dispatches type pars$ITNuse.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/UseBedNet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Model bed net usage, called from Behavior — UseBedNet","text":"","code":"UseBedNet(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/UseBedNet.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Model bed net usage, called from Behavior — UseBedNet","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/UseBedNet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Model bed net usage, called from Behavior — UseBedNet","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/UseBedNet.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Bed net ownership — UseBedNet.null","title":"Bed net ownership — UseBedNet.null","text":"Implements UseBedNet null model bed nets (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/UseBedNet.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bed net ownership — UseBedNet.null","text":"","code":"# S3 method for null UseBedNet(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/UseBedNet.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bed net ownership — UseBedNet.null","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/UseBedNet.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bed net ownership — UseBedNet.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.control.html","id":null,"dir":"Reference","previous_headings":"","what":"Distribute vector control, the null model — VectorControl.control","title":"Distribute vector control, the null model — VectorControl.control","text":"Implements VectorControl control model vector control (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Distribute vector control, the null model — VectorControl.control","text":"","code":"# S3 method for control VectorControl(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Distribute vector control, the null model — VectorControl.control","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.control.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Distribute vector control, the null model — VectorControl.control","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.html","id":null,"dir":"Reference","previous_headings":"","what":"Distribute vector control — VectorControl","title":"Distribute vector control — VectorControl","text":"method dispatches type pars$VECTOR_CONTROL.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Distribute vector control — VectorControl","text":"","code":"VectorControl(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Distribute vector control — VectorControl","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Distribute vector control — VectorControl","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Distribute vector control — VectorControl.null","title":"Distribute vector control — VectorControl.null","text":"Implements VectorControl null model vector control (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Distribute vector control — VectorControl.null","text":"","code":"# S3 method for null VectorControl(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Distribute vector control — VectorControl.null","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Distribute vector control — VectorControl.null","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.control.html","id":null,"dir":"Reference","previous_headings":"","what":"Distribute vector control, the null model — VectorControlEffectSizes.control","title":"Distribute vector control, the null model — VectorControlEffectSizes.control","text":"Implements VectorControlEffectSizes control model vector control (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Distribute vector control, the null model — VectorControlEffectSizes.control","text":"","code":"# S3 method for control VectorControlEffectSizes(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Distribute vector control, the null model — VectorControlEffectSizes.control","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.control.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Distribute vector control, the null model — VectorControlEffectSizes.control","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.html","id":null,"dir":"Reference","previous_headings":"","what":"Vector control effect sizes — VectorControlEffectSizes","title":"Vector control effect sizes — VectorControlEffectSizes","text":"method dispatches type pars$VECTOR_CONTROL.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Vector control effect sizes — VectorControlEffectSizes","text":"","code":"VectorControlEffectSizes(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Vector control effect sizes — VectorControlEffectSizes","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Vector control effect sizes — VectorControlEffectSizes","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Vector control effect sizes — VectorControlEffectSizes.null","title":"Vector control effect sizes — VectorControlEffectSizes.null","text":"Implements VectorControlEffectSizes null model vector control (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Vector control effect sizes — VectorControlEffectSizes.null","text":"","code":"# S3 method for null VectorControlEffectSizes(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Vector control effect sizes — VectorControlEffectSizes.null","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Vector control effect sizes — VectorControlEffectSizes.null","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.control.html","id":null,"dir":"Reference","previous_headings":"","what":"Vector control durability and effects — VectorControlEffects.control","title":"Vector control durability and effects — VectorControlEffects.control","text":"Implements VectorControlEffects control model vector control (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Vector control durability and effects — VectorControlEffects.control","text":"","code":"# S3 method for control VectorControlEffects(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Vector control durability and effects — VectorControlEffects.control","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.control.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Vector control durability and effects — VectorControlEffects.control","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.html","id":null,"dir":"Reference","previous_headings":"","what":"Vector control: durability & effects — VectorControlEffects","title":"Vector control: durability & effects — VectorControlEffects","text":"method dispatches type pars$VECTOR_CONTROL.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Vector control: durability & effects — VectorControlEffects","text":"","code":"VectorControlEffects(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Vector control: durability & effects — VectorControlEffects","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Vector control: durability & effects — VectorControlEffects","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Vector control: durability & effects — VectorControlEffects.null","title":"Vector control: durability & effects — VectorControlEffects.null","text":"Implements VectorControlEffects null model vector control (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Vector control: durability & effects — VectorControlEffects.null","text":"","code":"# S3 method for null VectorControlEffects(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Vector control: durability & effects — VectorControlEffects.null","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Vector control: durability & effects — VectorControlEffects.null","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Visitors, the basic model — Visitors.basic","title":"Visitors, the basic model — Visitors.basic","text":"Implements Visitors basic model Visitors","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Visitors, the basic model — Visitors.basic","text":"","code":"# S3 method for basic Visitors(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Visitors, the basic model — Visitors.basic","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Visitors, the basic model — Visitors.basic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.html","id":null,"dir":"Reference","previous_headings":"","what":"Visitors — Visitors","title":"Visitors — Visitors","text":"method dispatches type pars$VISITORS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Visitors — Visitors","text":"","code":"Visitors(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Visitors — Visitors","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Visitors — Visitors","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Visitors, a static model — Visitors.static","title":"Visitors, a static model — Visitors.static","text":"Implements Visitors static model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Visitors, a static model — Visitors.static","text":"","code":"# S3 method for static Visitors(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Visitors, a static model — Visitors.static","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Visitors, a static model — Visitors.static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing weather — Weather.forced","title":"Methods for exogenous variables describing weather — Weather.forced","text":"Implements exogenous forcing Weather","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing weather — Weather.forced","text":"","code":"# S3 method for forced Weather(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Weather.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing weather — Weather.forced","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing weather — Weather.forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing weather — Weather","title":"Methods for exogenous variables describing weather — Weather","text":"method dispatches type pars$WEATHER.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing weather — Weather","text":"","code":"Weather(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Weather.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing weather — Weather","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing weather — Weather","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing weather — Weather.null","title":"Methods for exogenous variables describing weather — Weather.null","text":"Implements Weather null model (variables)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing weather — Weather.null","text":"","code":"# S3 method for null Weather(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Weather.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing weather — Weather.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing weather — Weather.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/approx_equal.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if two numeric values are approximately equal — approx_equal","title":"Check if two numeric values are approximately equal — approx_equal","text":"Check two numeric values approximately equal","code":""},{"path":"https://dd-harp.github.io/exDE/reference/approx_equal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if two numeric values are approximately equal — approx_equal","text":"","code":"approx_equal(a, b, tol = sqrt(.Machine$double.eps))"},{"path":"https://dd-harp.github.io/exDE/reference/approx_equal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if two numeric values are approximately equal — approx_equal","text":"numeric object b numeric object tol numeric tolerance","code":""},{"path":"https://dd-harp.github.io/exDE/reference/approx_equal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if two numeric values are approximately equal — approx_equal","text":"logical value","code":""},{"path":"https://dd-harp.github.io/exDE/reference/checkIt.html","id":null,"dir":"Reference","previous_headings":"","what":"Check the length of an input value — checkIt","title":"Check the length of an input value — checkIt","text":"Check length input value","code":""},{"path":"https://dd-harp.github.io/exDE/reference/checkIt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check the length of an input value — checkIt","text":"","code":"checkIt(x, lng, type = \"numeric\", fixit = TRUE)"},{"path":"https://dd-harp.github.io/exDE/reference/checkIt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check the length of an input value — checkIt","text":"x numeric object lng numeric object type character string specifying required typeof fixit logical value, TRUE force length lng","code":""},{"path":"https://dd-harp.github.io/exDE/reference/checkIt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check the length of an input value — checkIt","text":"numeric object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Check abiotic — check_abiotic.forced","title":"Check abiotic — check_abiotic.forced","text":"Check abiotic","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check abiotic — check_abiotic.forced","text":"","code":"# S3 method for forced check_abiotic(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check abiotic — check_abiotic.forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check abiotic — check_abiotic.forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.html","id":null,"dir":"Reference","previous_headings":"","what":"Check abiotic — check_abiotic","title":"Check abiotic — check_abiotic","text":"Check abiotic","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check abiotic — check_abiotic","text":"","code":"check_abiotic(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check abiotic — check_abiotic","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check abiotic — check_abiotic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Check abiotic — check_abiotic.null","title":"Check abiotic — check_abiotic.null","text":"Check abiotic","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check abiotic — check_abiotic.null","text":"","code":"# S3 method for null check_abiotic(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check abiotic — check_abiotic.null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check abiotic — check_abiotic.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Check civil — check_civil.forced","title":"Check civil — check_civil.forced","text":"Check civil","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check civil — check_civil.forced","text":"","code":"# S3 method for forced check_civil(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check civil — check_civil.forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check civil — check_civil.forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.html","id":null,"dir":"Reference","previous_headings":"","what":"Check civil — check_civil","title":"Check civil — check_civil","text":"Check civil","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check civil — check_civil","text":"","code":"check_civil(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check civil — check_civil","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check civil — check_civil","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Check civil — check_civil.null","title":"Check civil — check_civil.null","text":"Check civil","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check civil — check_civil.null","text":"","code":"# S3 method for null check_civil(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check civil — check_civil.null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check civil — check_civil.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_AvailableHabitat.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute total availability of aquatic habitats — compute_AvailableHabitat","title":"Compute total availability of aquatic habitats — compute_AvailableHabitat","text":"Computes availability aquatic habitats","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_AvailableHabitat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute total availability of aquatic habitats — compute_AvailableHabitat","text":"","code":"compute_AvailableHabitat(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_AvailableHabitat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute total availability of aquatic habitats — compute_AvailableHabitat","text":"pars list s vector species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_AvailableHabitat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute total availability of aquatic habitats — compute_AvailableHabitat","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_AvailableHosts.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute availability blood hosts of the i^th species — compute_AvailableHosts","title":"Compute availability blood hosts of the i^th species — compute_AvailableHosts","text":"Compute availability pathogen's hosts blood feeding","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_AvailableHosts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute availability blood hosts of the i^th species — compute_AvailableHosts","text":"","code":"compute_AvailableHosts(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_AvailableHosts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute availability blood hosts of the i^th species — compute_AvailableHosts","text":"t current simulation time y state vector pars list s vector species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_AvailableHosts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute availability blood hosts of the i^th species — compute_AvailableHosts","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute EIR — compute_EIR","title":"Compute EIR — compute_EIR","text":"function computes EIR stratum host species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute EIR — compute_EIR","text":"","code":"compute_EIR(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_EIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute EIR — compute_EIR","text":"t current simulation time y state vector pars, list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute EIR — compute_EIR","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EIR_full.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute EIR for each vector-host pair — compute_EIR_full","title":"Compute EIR for each vector-host pair — compute_EIR_full","text":"function computes EIR vector species stratum host species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EIR_full.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute EIR for each vector-host pair — compute_EIR_full","text":"","code":"compute_EIR_full(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_EIR_full.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute EIR for each vector-host pair — compute_EIR_full","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EIR_full.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute EIR for each vector-host pair — compute_EIR_full","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EggsLaid.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute eggs laid — compute_EggsLaid","title":"Compute eggs laid — compute_EggsLaid","text":"Computes eggs laid s^th species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EggsLaid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute eggs laid — compute_EggsLaid","text":"","code":"compute_EggsLaid(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_EggsLaid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute eggs laid — compute_EggsLaid","text":"t time y state variables pars model object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EggsLaid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute eggs laid — compute_EggsLaid","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_NI.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the NI — compute_NI","title":"Compute the NI — compute_NI","text":"Using output deSolve::ode deSolve::dede, compute NI stratum","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_NI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the NI — compute_NI","text":"","code":"compute_NI(deout, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_NI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the NI — compute_NI","text":"deout matrix, output deSolve pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_NI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the NI — compute_NI","text":"numeric containing NI","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_NI_ix.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute NI once — compute_NI_ix","title":"Compute NI once — compute_NI_ix","text":"Using output deSolve::ode deSolve::dede, compute NI point time","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_NI_ix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute NI once — compute_NI_ix","text":"","code":"compute_NI_ix(ix, deout, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_NI_ix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute NI once — compute_NI_ix","text":"ix integer deout matrix, output deSolve pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_NI_ix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute NI once — compute_NI_ix","text":"list containing NI","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_beta.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute beta — compute_beta","title":"Compute beta — compute_beta","text":"function computes mixing matrix, beta","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_beta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute beta — compute_beta","text":"","code":"compute_beta(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_beta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute beta — compute_beta","text":"t current simulation time y state vector pars, list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_beta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute beta — compute_beta","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_calU.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute calU — compute_calU","title":"Compute calU — compute_calU","text":"Computes egg laying matrices","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_calU.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute calU — compute_calU","text":"","code":"compute_calU(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_calU.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute calU — compute_calU","text":"t time y state variables pars model object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_calU.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute calU — compute_calU","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqM.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the fqM — compute_fqM","title":"Compute the fqM — compute_fqM","text":"Using output deSolve::ode deSolve::dede, compute fqM every point time","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the fqM — compute_fqM","text":"","code":"compute_fqM(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the fqM — compute_fqM","text":"deout matrix, output deSolve pars list s vector species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the fqM — compute_fqM","text":"vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqM_ix.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the fqM for the ith — compute_fqM_ix","title":"Compute the fqM for the ith — compute_fqM_ix","text":"Using output deSolve::ode deSolve::dede, compute fqM one point time","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqM_ix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the fqM for the ith — compute_fqM_ix","text":"","code":"compute_fqM_ix(ix, deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqM_ix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the fqM for the ith — compute_fqM_ix","text":"ix integer deout matrix, output deSolve pars list s vector species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqM_ix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the fqM for the ith — compute_fqM_ix","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the fqZ — compute_fqZ","title":"Compute the fqZ — compute_fqZ","text":"Using output deSolve::ode deSolve::dede, compute fqZ every point time","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the fqZ — compute_fqZ","text":"","code":"compute_fqZ(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the fqZ — compute_fqZ","text":"deout matrix, output deSolve pars list s vector species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqZ.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the fqZ — compute_fqZ","text":"vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqZ_ix.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the fqZ for the ith — compute_fqZ_ix","title":"Compute the fqZ for the ith — compute_fqZ_ix","text":"Using output deSolve::ode deSolve::dede, compute fqZ one point time","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqZ_ix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the fqZ for the ith — compute_fqZ_ix","text":"","code":"compute_fqZ_ix(ix, deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqZ_ix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the fqZ for the ith — compute_fqZ_ix","text":"ix integer deout matrix, output deSolve pars list s vector species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqZ_ix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the fqZ for the ith — compute_fqZ_ix","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_kappa.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute kappa — compute_kappa","title":"Compute kappa — compute_kappa","text":"function computes kappa vector species patch","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_kappa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute kappa — compute_kappa","text":"","code":"compute_kappa(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_kappa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute kappa — compute_kappa","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_kappa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute kappa — compute_kappa","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_local_frac.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the local fraction — compute_local_frac","title":"Compute the local fraction — compute_local_frac","text":"Compute availability pathogen's hosts blood feeding","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_local_frac.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the local fraction — compute_local_frac","text":"","code":"compute_local_frac(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_local_frac.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the local fraction — compute_local_frac","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_local_frac.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the local fraction — compute_local_frac","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.cohort.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute dynamical terms — compute_terms.cohort","title":"Compute dynamical terms — compute_terms.cohort","text":"Using output deSolve compute dynamical terms output xde_solve.cohort","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.cohort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute dynamical terms — compute_terms.cohort","text":"","code":"# S3 method for cohort compute_terms(varslist, deout, pars, s, i)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.cohort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute dynamical terms — compute_terms.cohort","text":"varslist list variable names attached deout matrix, output deSolve pars list s vector species index host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.cohort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute dynamical terms — compute_terms.cohort","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute dynamical terms — compute_terms","title":"Compute dynamical terms — compute_terms","text":"Using output deSolve compute dynamical terms every point time. method dispatches type pars$compute.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute dynamical terms — compute_terms","text":"","code":"compute_terms(varslist, deout, pars, s, i)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute dynamical terms — compute_terms","text":"varslist list variable names attached deout matrix, output deSolve pars list s vector species index host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute dynamical terms — compute_terms","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.human.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute dynamical terms — compute_terms.human","title":"Compute dynamical terms — compute_terms.human","text":"Using output deSolve compute dynamical terms output xde_solve.human","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.human.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute dynamical terms — compute_terms.human","text":"","code":"# S3 method for human compute_terms(varslist, deout, pars, s, i)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.human.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute dynamical terms — compute_terms.human","text":"varslist list variable names attached deout matrix, output deSolve pars list s vector species index host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.human.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute dynamical terms — compute_terms.human","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.na.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute dynamical terms — compute_terms.na","title":"Compute dynamical terms — compute_terms.na","text":"Using output deSolve compute dynamical terms output xde_solve relevant dynamical terms","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute dynamical terms — compute_terms.na","text":"","code":"# S3 method for na compute_terms(varslist, deout, pars, s, i)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute dynamical terms — compute_terms.na","text":"varslist list variable names attached deout matrix, output deSolve pars list s vector species index host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute dynamical terms — compute_terms.na","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.xde.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute dynamical terms — compute_terms.xde","title":"Compute dynamical terms — compute_terms.xde","text":"Using output deSolve compute dynamical terms output xde_solve.ode xde_solve.dde","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.xde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute dynamical terms — compute_terms.xde","text":"","code":"# S3 method for xde compute_terms(varslist, deout, pars, s, i)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.xde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute dynamical terms — compute_terms.xde","text":"varslist list variable names attached deout matrix, output deSolve pars list s vector species index host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.xde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute dynamical terms — compute_terms.xde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms_steady.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute dynamical terms — compute_terms_steady","title":"Compute dynamical terms — compute_terms_steady","text":"Using output deSolve compute dynamical terms output root_solve","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms_steady.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute dynamical terms — compute_terms_steady","text":"","code":"compute_terms_steady(varslist, y_eq, pars, s, i)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms_steady.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute dynamical terms — compute_terms_steady","text":"varslist list variable names attached y_eq matrix, output rootSolve pars list s vector species index host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms_steady.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute dynamical terms — compute_terms_steady","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dEIPdt.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the derivative of the EIP as a function of time — dEIPdt","title":"Compute the derivative of the EIP as a function of time — dEIPdt","text":"method dispatches type EIPmod.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dEIPdt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the derivative of the EIP as a function of time — dEIPdt","text":"","code":"dEIPdt(t, EIPmod)"},{"path":"https://dd-harp.github.io/exDE/reference/dEIPdt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the derivative of the EIP as a function of time — dEIPdt","text":"t current simulation time EIPmod list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dEIPdt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the derivative of the EIP as a function of time — dEIPdt","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dEIPdt.static.html","id":null,"dir":"Reference","previous_headings":"","what":"This function computes the negative derivative of the EIP as a function of time — dEIPdt.static","title":"This function computes the negative derivative of the EIP as a function of time — dEIPdt.static","text":"Implements dEIPdt static model (dEIPdt=0)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dEIPdt.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function computes the negative derivative of the EIP as a function of time — dEIPdt.static","text":"","code":"# S3 method for static dEIPdt(t, EIPmod)"},{"path":"https://dd-harp.github.io/exDE/reference/dEIPdt.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"This function computes the negative derivative of the EIP as a function of time — dEIPdt.static","text":"t current simulation time EIPmod list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dEIPdt.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"This function computes the negative derivative of the EIP as a function of time — dEIPdt.static","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dHdt.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives of demographic changes in human populations — dHdt","title":"Derivatives of demographic changes in human populations — dHdt","text":"method dispatches type pars$Hpar$dH","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dHdt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives of demographic changes in human populations — dHdt","text":"","code":"dHdt(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/dHdt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives of demographic changes in human populations — dHdt","text":"t current simulation time y state vector pars list index host species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dHdt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives of demographic changes in human populations — dHdt","text":"see help pages specific methods","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dHdt.zero.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives of demographic changes in human populations — dHdt.zero","title":"Derivatives of demographic changes in human populations — dHdt.zero","text":"Implements dHdt y static","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dHdt.zero.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives of demographic changes in human populations — dHdt.zero","text":"","code":"# S3 method for zero dHdt(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/dHdt.zero.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives of demographic changes in human populations — dHdt.zero","text":"t current simulation time y state vector pars list index host species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dHdt.zero.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives of demographic changes in human populations — dHdt.zero","text":"numeric vector 0s","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for aquatic stage mosquitoes — dLdt.basic","title":"Derivatives for aquatic stage mosquitoes — dLdt.basic","text":"Implements dLdt basic competition model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for aquatic stage mosquitoes — dLdt.basic","text":"","code":"# S3 method for basic dLdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for aquatic stage mosquitoes — dLdt.basic","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for aquatic stage mosquitoes — dLdt.basic","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for aquatic stage mosquitoes — dLdt","title":"Derivatives for aquatic stage mosquitoes — dLdt","text":"method dispatches type pars$Lpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for aquatic stage mosquitoes — dLdt","text":"","code":"dLdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for aquatic stage mosquitoes — dLdt","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for aquatic stage mosquitoes — dLdt","text":"numeric vector length pars$L_ix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for aquatic stage mosquitoes — dLdt.trace","title":"Derivatives for aquatic stage mosquitoes — dLdt.trace","text":"Implements dLdt trace (forced emergence) model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for aquatic stage mosquitoes — dLdt.trace","text":"","code":"# S3 method for trace dLdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for aquatic stage mosquitoes — dLdt.trace","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for aquatic stage mosquitoes — dLdt.trace","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.GeRM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for adult mosquitoes — dMYZdt.GeRM_dde","title":"Derivatives for adult mosquitoes — dMYZdt.GeRM_dde","text":"Implements dMYZdt GeRM DDE model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.GeRM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for adult mosquitoes — dMYZdt.GeRM_dde","text":"","code":"# S3 method for GeRM_dde dMYZdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.GeRM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for adult mosquitoes — dMYZdt.GeRM_dde","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.GeRM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for adult mosquitoes — dMYZdt.GeRM_dde","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.GeRM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for adult mosquitoes — dMYZdt.GeRM_ode","title":"Derivatives for adult mosquitoes — dMYZdt.GeRM_ode","text":"Implements dMYZdt GeRM ODE model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.GeRM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for adult mosquitoes — dMYZdt.GeRM_ode","text":"","code":"# S3 method for GeRM_ode dMYZdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.GeRM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for adult mosquitoes — dMYZdt.GeRM_ode","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.GeRM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for adult mosquitoes — dMYZdt.GeRM_ode","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.Gtrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for aquatic stage mosquitoes — dMYZdt.Gtrace","title":"Derivatives for aquatic stage mosquitoes — dMYZdt.Gtrace","text":"Implements dMYZdt Gtrace (forced emergence) model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.Gtrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for aquatic stage mosquitoes — dMYZdt.Gtrace","text":"","code":"# S3 method for Gtrace dMYZdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.Gtrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for aquatic stage mosquitoes — dMYZdt.Gtrace","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for aquatic stage mosquitoes — dMYZdt.Gtrace","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.RM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for adult mosquitoes — dMYZdt.RM_dde","title":"Derivatives for adult mosquitoes — dMYZdt.RM_dde","text":"Implements dMYZdt RM DDE model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.RM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for adult mosquitoes — dMYZdt.RM_dde","text":"","code":"# S3 method for RM_dde dMYZdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.RM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for adult mosquitoes — dMYZdt.RM_dde","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.RM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for adult mosquitoes — dMYZdt.RM_dde","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.RM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for adult mosquitoes — dMYZdt.RM_ode","title":"Derivatives for adult mosquitoes — dMYZdt.RM_ode","text":"Implements dMYZdt RM ODE model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.RM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for adult mosquitoes — dMYZdt.RM_ode","text":"","code":"# S3 method for RM_ode dMYZdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.RM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for adult mosquitoes — dMYZdt.RM_ode","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.RM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for adult mosquitoes — dMYZdt.RM_ode","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for aquatic stage mosquitoes — dMYZdt.Ztrace","title":"Derivatives for aquatic stage mosquitoes — dMYZdt.Ztrace","text":"Implements dMYZdt Ztrace (forced emergence) model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for aquatic stage mosquitoes — dMYZdt.Ztrace","text":"","code":"# S3 method for Ztrace dMYZdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for aquatic stage mosquitoes — dMYZdt.Ztrace","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for aquatic stage mosquitoes — dMYZdt.Ztrace","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for adult mosquitoes — dMYZdt.basicM","title":"Derivatives for adult mosquitoes — dMYZdt.basicM","text":"Implements dMYZdt basicM ODE model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for adult mosquitoes — dMYZdt.basicM","text":"","code":"# S3 method for basicM dMYZdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for adult mosquitoes — dMYZdt.basicM","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for adult mosquitoes — dMYZdt.basicM","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for adult mosquitoes — dMYZdt","title":"Derivatives for adult mosquitoes — dMYZdt","text":"method dispatches type pars$MYZpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for adult mosquitoes — dMYZdt","text":"","code":"dMYZdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for adult mosquitoes — dMYZdt","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for adult mosquitoes — dMYZdt","text":"derivatives vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.SIP","title":"Derivatives for human population — dXdt.SIP","text":"Implements dXdt SIP model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.SIP","text":"","code":"# S3 method for SIP dXdt(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.SIP","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.SIP","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.SIS","title":"Derivatives for human population — dXdt.SIS","text":"Implements dXdt SIS model, demography.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.SIS","text":"","code":"# S3 method for SIS dXdt(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.SIS","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.SIS","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.hMoI","title":"Derivatives for human population — dXdt.hMoI","text":"Implements dXdt hybrid MoI model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.hMoI","text":"","code":"# S3 method for hMoI dXdt(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.hMoI","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.hMoI","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt","title":"Derivatives for human population — dXdt","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt","text":"","code":"dXdt(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.trace","title":"Derivatives for human population — dXdt.trace","text":"Implements dXdt trace model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.trace","text":"","code":"# S3 method for trace dXdt(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.trace","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.trace","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dde2ode_MYZ.dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a model from dde to the corresponding ode — dde2ode_MYZ.dde","title":"Convert a model from dde to the corresponding ode — dde2ode_MYZ.dde","text":"dde, return corresponding ode","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dde2ode_MYZ.dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a model from dde to the corresponding ode — dde2ode_MYZ.dde","text":"","code":"# S3 method for dde dde2ode_MYZ(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/dde2ode_MYZ.dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a model from dde to the corresponding ode — dde2ode_MYZ.dde","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dde2ode_MYZ.dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a model from dde to the corresponding ode — dde2ode_MYZ.dde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dde2ode_MYZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a model from dde to the corresponding ode — dde2ode_MYZ","title":"Convert a model from dde to the corresponding ode — dde2ode_MYZ","text":"method dispatches type pars$MYZpar$xde","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dde2ode_MYZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a model from dde to the corresponding ode — dde2ode_MYZ","text":"","code":"dde2ode_MYZ(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/dde2ode_MYZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a model from dde to the corresponding ode — dde2ode_MYZ","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dde2ode_MYZ.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a model from dde to the corresponding ode — dde2ode_MYZ","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dde2ode_MYZ.ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a model from dde to the corresponding ode — dde2ode_MYZ.ode","title":"Convert a model from dde to the corresponding ode — dde2ode_MYZ.ode","text":"already ode, return pars unchanged.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dde2ode_MYZ.ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a model from dde to the corresponding ode — dde2ode_MYZ.ode","text":"","code":"# S3 method for ode dde2ode_MYZ(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/dde2ode_MYZ.ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a model from dde to the corresponding ode — dde2ode_MYZ.ode","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dde2ode_MYZ.ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a model from dde to the corresponding ode — dde2ode_MYZ.ode","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/diag_inverse.html","id":null,"dir":"Reference","previous_headings":"","what":"Invert a diagonal matrix — diag_inverse","title":"Invert a diagonal matrix — diag_inverse","text":"Invert diagonal matrix passed vector. elements zero, set one.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/diag_inverse.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Invert a diagonal matrix — diag_inverse","text":"","code":"diag_inverse(x)"},{"path":"https://dd-harp.github.io/exDE/reference/diag_inverse.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Invert a diagonal matrix — diag_inverse","text":"x numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/diag_inverse.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Invert a diagonal matrix — diag_inverse","text":"diagonal matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the initial values as a vector — get_inits","title":"Get the initial values as a vector — get_inits","text":"Get initial values vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the initial values as a vector — get_inits","text":"","code":"get_inits(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the initial values as a vector — get_inits","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the initial values as a vector — get_inits","text":"y numeric vector assigned class \"dynamic\"","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_L.basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_L.basic","title":"Return initial values as a vector — get_inits_L.basic","text":"Implements get_inits_L GeRM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_L.basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_L.basic","text":"","code":"# S3 method for basic get_inits_L(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_L.basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_L.basic","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_L.basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_L.basic","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_L.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_L","title":"Return initial values as a vector — get_inits_L","text":"method dispatches type pars$Lpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_L.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_L","text":"","code":"get_inits_L(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_L.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_L","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_L.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_L","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_L.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_L.trace","title":"Return initial values as a vector — get_inits_L.trace","text":"Implements get_inits_L GeRM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_L.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_L.trace","text":"","code":"# S3 method for trace get_inits_L(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_L.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_L.trace","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_L.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_L.trace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.GeRM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_MYZ.GeRM_dde","title":"Return initial values as a vector — get_inits_MYZ.GeRM_dde","text":"Implements get_inits_MYZ GeRM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.GeRM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_MYZ.GeRM_dde","text":"","code":"# S3 method for GeRM_dde get_inits_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.GeRM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_MYZ.GeRM_dde","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.GeRM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_MYZ.GeRM_dde","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.GeRM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_MYZ.GeRM_ode","title":"Return initial values as a vector — get_inits_MYZ.GeRM_ode","text":"Implements get_inits_MYZ GeRM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.GeRM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_MYZ.GeRM_ode","text":"","code":"# S3 method for GeRM_ode get_inits_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.GeRM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_MYZ.GeRM_ode","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.GeRM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_MYZ.GeRM_ode","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.Gtrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_MYZ.Gtrace","title":"Return initial values as a vector — get_inits_MYZ.Gtrace","text":"Implements get_inits_MYZ GeRM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.Gtrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_MYZ.Gtrace","text":"","code":"# S3 method for Gtrace get_inits_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.Gtrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_MYZ.Gtrace","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_MYZ.Gtrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.RM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_MYZ.RM_dde","title":"Return initial values as a vector — get_inits_MYZ.RM_dde","text":"Implements get_inits_MYZ RM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.RM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_MYZ.RM_dde","text":"","code":"# S3 method for RM_dde get_inits_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.RM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_MYZ.RM_dde","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.RM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_MYZ.RM_dde","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.RM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_MYZ.RM_ode","title":"Return initial values as a vector — get_inits_MYZ.RM_ode","text":"Implements get_inits_MYZ RM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.RM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_MYZ.RM_ode","text":"","code":"# S3 method for RM_ode get_inits_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.RM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_MYZ.RM_ode","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.RM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_MYZ.RM_ode","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_MYZ.Ztrace","title":"Return initial values as a vector — get_inits_MYZ.Ztrace","text":"Implements get_inits_MYZ GeRM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_MYZ.Ztrace","text":"","code":"# S3 method for Ztrace get_inits_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_MYZ.Ztrace","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_MYZ.Ztrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_MYZ.basicM","title":"Return initial values as a vector — get_inits_MYZ.basicM","text":"Implements get_inits_MYZ basicM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_MYZ.basicM","text":"","code":"# S3 method for basicM get_inits_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_MYZ.basicM","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_MYZ.basicM","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_MYZ","title":"Return initial values as a vector — get_inits_MYZ","text":"method dispatches type pars$MYZpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_MYZ","text":"","code":"get_inits_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_MYZ","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_MYZ","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_X.SIP","title":"Return initial values as a vector — get_inits_X.SIP","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_X.SIP","text":"","code":"# S3 method for SIP get_inits_X(pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_X.SIP","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_X.SIP","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_X.SIS","title":"Return initial values as a vector — get_inits_X.SIS","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_X.SIS","text":"","code":"# S3 method for SIS get_inits_X(pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_X.SIS","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_X.SIS","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_X.hMoI","title":"Return initial values as a vector — get_inits_X.hMoI","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_X.hMoI","text":"","code":"# S3 method for hMoI get_inits_X(pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_X.hMoI","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_X.hMoI","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_X","title":"Return initial values as a vector — get_inits_X","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_X","text":"","code":"get_inits_X(pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_X","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_X","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_X.trace","title":"Return initial values as a vector — get_inits_X.trace","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_X.trace","text":"","code":"# S3 method for trace get_inits_X(pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_X.trace","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_X.trace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/last_to_inits.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the initial values to the last values of the last simulation — last_to_inits","title":"Set the initial values to the last values of the last simulation — last_to_inits","text":"Set initial values last values last simulation","code":""},{"path":"https://dd-harp.github.io/exDE/reference/last_to_inits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the initial values to the last values of the last simulation — last_to_inits","text":"","code":"last_to_inits(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/last_to_inits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the initial values to the last values of the last simulation — last_to_inits","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/last_to_inits.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the initial values to the last values of the last simulation — last_to_inits","text":"y numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Hpar_trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for human null model — make_Hpar_trace","title":"Make parameters for human null model — make_Hpar_trace","text":"Make parameters human null model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Hpar_trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for human null model — make_Hpar_trace","text":"","code":"make_Hpar_trace(nPatches, Hopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_Hpar_trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for human null model — make_Hpar_trace","text":"nPatches number patches model Hopts list overwrite defaults","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Hpar_trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for human null model — make_Hpar_trace","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Linits_basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for basic competition aquatic mosquito model — make_Linits_basic","title":"Make inits for basic competition aquatic mosquito model — make_Linits_basic","text":"Make inits basic competition aquatic mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Linits_basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for basic competition aquatic mosquito model — make_Linits_basic","text":"","code":"make_Linits_basic(nHabitats, Lopts = list(), L0 = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Linits_basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for basic competition aquatic mosquito model — make_Linits_basic","text":"nHabitats number habitats model Lopts list overwrites default values L0 initial conditions","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Linits_basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for basic competition aquatic mosquito model — make_Linits_basic","text":"list Linits added","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Lpar_basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for basic competition aquatic mosquito model — make_Lpar_basic","title":"Make parameters for basic competition aquatic mosquito model — make_Lpar_basic","text":"Make parameters basic competition aquatic mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Lpar_basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for basic competition aquatic mosquito model — make_Lpar_basic","text":"","code":"make_Lpar_basic(nHabitats, Lopts = list(), psi = 1/8, phi = 1/8, theta = 1/100)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Lpar_basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for basic competition aquatic mosquito model — make_Lpar_basic","text":"nHabitats number habitats model Lopts list overwrites default values psi maturation rates aquatic habitat phi density-independent mortality rates aquatic habitat theta density-dependent mortality terms aquatic habitat","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Lpar_basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for basic competition aquatic mosquito model — make_Lpar_basic","text":"list Lpar added","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Lpar_trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for trace aquatic mosquito model — make_Lpar_trace","title":"Make parameters for trace aquatic mosquito model — make_Lpar_trace","text":"Make parameters trace aquatic mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Lpar_trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for trace aquatic mosquito model — make_Lpar_trace","text":"","code":"make_Lpar_trace(nHabitats, Lopts = list(), Lambda = 1000, Lt = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Lpar_trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for trace aquatic mosquito model — make_Lpar_trace","text":"nHabitats number habitats model Lopts list overwrites default values Lambda vector mean emergence rates aquatic habitat Lt function form Lt(t,pars) computes temporal fluctuations","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Lpar_trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for trace aquatic mosquito model — make_Lpar_trace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_GeRM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_dde","title":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_dde","text":"Make inits GeRM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_GeRM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_dde","text":"","code":"make_MYZinits_GeRM_dde(   nPatches,   Upsilon,   MYZopts = list(),   M0 = 5,   G0 = 1,   Y0 = 1,   Z0 = 1 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_GeRM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_dde","text":"nPatches number patches model Upsilon matrix describing survival dispersal EIP MYZopts list values overwrites defaults M0 total mosquito density patch G0 total parous mosquito density patch Y0 infected mosquito density patch Z0 infectious mosquito density patch","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_GeRM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_dde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_GeRM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_ode","title":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_ode","text":"Make inits GeRM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_GeRM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_ode","text":"","code":"make_MYZinits_GeRM_ode(   nPatches,   MYZopts = list(),   M0 = 5,   G0 = 1,   Y0 = 1,   Z0 = 1 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_GeRM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_ode","text":"nPatches number patches model MYZopts list values overwrites defaults M0 total mosquito density patch G0 total parous mosquito density patch Y0 infected mosquito density patch Z0 infectious mosquito density patch","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_GeRM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_ode","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_RM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for RM adult mosquito model — make_MYZinits_RM_dde","title":"Make inits for RM adult mosquito model — make_MYZinits_RM_dde","text":"Make inits RM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_RM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for RM adult mosquito model — make_MYZinits_RM_dde","text":"","code":"make_MYZinits_RM_dde(   nPatches,   Upsilon,   MYZopts = list(),   M0 = 5,   P0 = 1,   Y0 = 1,   Z0 = 1 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_RM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for RM adult mosquito model — make_MYZinits_RM_dde","text":"nPatches number patches model Upsilon matrix describing survival dispersal EIP MYZopts list values overwrites defaults M0 total mosquito density patch P0 total parous mosquito density patch Y0 infected mosquito density patch Z0 infectious mosquito density patch","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_RM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for RM adult mosquito model — make_MYZinits_RM_dde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_RM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for RM adult mosquito model — make_MYZinits_RM_ode","title":"Make inits for RM adult mosquito model — make_MYZinits_RM_ode","text":"Make inits RM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_RM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for RM adult mosquito model — make_MYZinits_RM_ode","text":"","code":"make_MYZinits_RM_ode(   nPatches,   MYZopts = list(),   M0 = 5,   P0 = 1,   Y0 = 1,   Z0 = 1 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_RM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for RM adult mosquito model — make_MYZinits_RM_ode","text":"nPatches number patches model MYZopts list values overwrites defaults M0 total mosquito density patch P0 total parous mosquito density patch Y0 infected mosquito density patch Z0 infectious mosquito density patch","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_RM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for RM adult mosquito model — make_MYZinits_RM_ode","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for basicM adult mosquito model — make_MYZinits_basicM","title":"Make inits for basicM adult mosquito model — make_MYZinits_basicM","text":"Make inits basicM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for basicM adult mosquito model — make_MYZinits_basicM","text":"","code":"make_MYZinits_basicM(nPatches, MYZopts = list(), M0 = 5, P0 = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for basicM adult mosquito model — make_MYZinits_basicM","text":"nPatches number patches model MYZopts list values overwrites defaults M0 total mosquito density patch P0 total parous mosquito density patch","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for basicM adult mosquito model — make_MYZinits_basicM","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_GeRM.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for GeRM ODE adult mosquito model — make_MYZpar_GeRM","title":"Make parameters for GeRM ODE adult mosquito model — make_MYZpar_GeRM","text":"Make parameters GeRM ODE adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_GeRM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for GeRM ODE adult mosquito model — make_MYZpar_GeRM","text":"","code":"make_MYZpar_GeRM(   nPatches,   MYZopts = list(),   EIPmod,   calK,   g = 1/12,   g_par = list(),   sigma = 1/8,   sigma_par = list(),   f = 0.3,   f_par = list(),   q = 0.95,   q_par = list(),   nu = 1,   nu_par = list(),   eggsPerBatch = 60 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_GeRM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for GeRM ODE adult mosquito model — make_MYZpar_GeRM","text":"nPatches number patches, integer MYZopts list values overwrites defaults EIPmod list defines EIP model calK mosquito dispersal matrix dimensions nPatches nPatches g mosquito mortality rate g_par parameters configure F_g sigma emigration rate sigma_par parameters configure F_sigma f feeding rate f_par parameters configure F_f q human blood fraction q_par parameters configure F_q nu oviposition rate, per mosquito nu_par parameters configure F_nu eggsPerBatch eggs laid per oviposition","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_GeRM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for GeRM ODE adult mosquito model — make_MYZpar_GeRM","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_Gtrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for Gtrace aquatic mosquito model — make_MYZpar_Gtrace","title":"Make parameters for Gtrace aquatic mosquito model — make_MYZpar_Gtrace","text":"Make parameters Gtrace aquatic mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_Gtrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for Gtrace aquatic mosquito model — make_MYZpar_Gtrace","text":"","code":"make_MYZpar_Gtrace(nPatches, MYZopts, Gm = 1, Gf = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_Gtrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for Gtrace aquatic mosquito model — make_MYZpar_Gtrace","text":"nPatches number patches model MYZopts list overwrite defaults Gm vector mean mosquito densities Gf function form Gf(t, pars) computes temporal fluctuations","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for Gtrace aquatic mosquito model — make_MYZpar_Gtrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for RM ODE adult mosquito model — make_MYZpar_RM","title":"Make parameters for RM ODE adult mosquito model — make_MYZpar_RM","text":"Make parameters RM ODE adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for RM ODE adult mosquito model — make_MYZpar_RM","text":"","code":"make_MYZpar_RM(   nPatches,   MYZopts = list(),   EIPmod,   calK,   g = 1/12,   sigma = 1/8,   f = 0.3,   q = 0.95,   nu = 1,   eggsPerBatch = 60 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for RM ODE adult mosquito model — make_MYZpar_RM","text":"nPatches number patches, integer MYZopts list values overwrites defaults EIPmod list defines EIP model calK mosquito dispersal matrix dimensions nPatches nPatches g mosquito mortality rate sigma emigration rate f feeding rate q human blood fraction nu oviposition rate, per mosquito eggsPerBatch eggs laid per oviposition","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_RM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for RM ODE adult mosquito model — make_MYZpar_RM","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for Ztrace aquatic mosquito model — make_MYZpar_Ztrace","title":"Make parameters for Ztrace aquatic mosquito model — make_MYZpar_Ztrace","text":"Make parameters Ztrace aquatic mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for Ztrace aquatic mosquito model — make_MYZpar_Ztrace","text":"","code":"make_MYZpar_Ztrace(nPatches, MYZopts, f = 0.3, q = 0.95, Zm = 1, Zf = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for Ztrace aquatic mosquito model — make_MYZpar_Ztrace","text":"nPatches integer MYZopts list values overwrites defaults f blood feeding rate q human fraction Zm vector mean mosquito densities Zf function form Zf(t, pars) computes temporal fluctuations","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for Ztrace aquatic mosquito model — make_MYZpar_Ztrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for basicM ODE adult mosquito model — make_MYZpar_basicM","title":"Make parameters for basicM ODE adult mosquito model — make_MYZpar_basicM","text":"Make parameters basicM ODE adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for basicM ODE adult mosquito model — make_MYZpar_basicM","text":"","code":"make_MYZpar_basicM(   nPatches,   MYZopts = list(),   calK,   g = 1/12,   sigma = 1/8,   f = 0.3,   q = 0.95,   nu = 1,   eggsPerBatch = 60 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for basicM ODE adult mosquito model — make_MYZpar_basicM","text":"nPatches number patches MYZopts list values overwrites defaults calK mosquito dispersal matrix dimensions nPatches nPatches g mosquito mortality rate sigma emigration rate f blood feeding rate q human blood feeding fraction nu oviposition rate, per mosquito eggsPerBatch eggs laid per oviposition","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for basicM ODE adult mosquito model — make_MYZpar_basicM","text":"list configured MYZpar","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Omega.html","id":null,"dir":"Reference","previous_headings":"","what":"Make the mosquito demography matrix — make_Omega","title":"Make the mosquito demography matrix — make_Omega","text":"Make mosquito demography matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Omega.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make the mosquito demography matrix — make_Omega","text":"","code":"make_Omega(g, sigma, K, nPatches)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Omega.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make the mosquito demography matrix — make_Omega","text":"g mortality rate sigma emigration  rate K mosquito dispersal matrix nPatches number patches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Omega.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make the mosquito demography matrix — make_Omega","text":"matrix dimensions nPatches nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TaR.html","id":null,"dir":"Reference","previous_headings":"","what":"Make TaR — make_TaR","title":"Make TaR — make_TaR","text":"Make time risk matrix (TaR) time spent matrix circadian function","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TaR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make TaR — make_TaR","text":"","code":"make_TaR(t, pars, i, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_TaR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make TaR — make_TaR","text":"t time pars list host species index s vector species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TaR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make TaR — make_TaR","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.as_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Pass a pre-configured TimeSpent — make_TimeSpent.as_matrix","title":"Pass a pre-configured TimeSpent — make_TimeSpent.as_matrix","text":"Implements make_TimeSpent as_matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.as_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pass a pre-configured TimeSpent — make_TimeSpent.as_matrix","text":"","code":"# S3 method for as_matrix make_TimeSpent(pars, i, TimeSpent, opts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.as_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pass a pre-configured TimeSpent — make_TimeSpent.as_matrix","text":"pars list host species index TimeSpent matrix; string opts list options configure TimeSpent","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.as_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pass a pre-configured TimeSpent — make_TimeSpent.as_matrix","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.athome.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a mosquito dispersal matrix, called TimeSpent with a here / away — make_TimeSpent.athome","title":"Make a mosquito dispersal matrix, called TimeSpent with a here / away — make_TimeSpent.athome","text":"Implements make_TimeSpent as_matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.athome.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a mosquito dispersal matrix, called TimeSpent with a here / away — make_TimeSpent.athome","text":"","code":"# S3 method for athome make_TimeSpent(pars, i, TimeSpent = \"athome\", opts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.athome.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a mosquito dispersal matrix, called TimeSpent with a here / away — make_TimeSpent.athome","text":"pars list host species index TimeSpent matrix; string opts list options configure TimeSpent","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.athome.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a mosquito dispersal matrix, called TimeSpent with a here / away — make_TimeSpent.athome","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a time spent matrix, called TimeSpent — make_TimeSpent","title":"Make a time spent matrix, called TimeSpent — make_TimeSpent","text":"Make time spent matrix, called TimeSpent","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a time spent matrix, called TimeSpent — make_TimeSpent","text":"","code":"make_TimeSpent(pars, i, TimeSpent, opts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a time spent matrix, called TimeSpent — make_TimeSpent","text":"pars list host species index TimeSpent matrix; string opts list options configure TimeSpent","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a time spent matrix, called TimeSpent — make_TimeSpent","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.xy.html","id":null,"dir":"Reference","previous_headings":"","what":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_TimeSpent.xy","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_TimeSpent.xy","text":"Implements make_TimeSpent kernels","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.xy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_TimeSpent.xy","text":"","code":"# S3 method for xy make_TimeSpent(pars, i, TimeSpent = \"xy\", opts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.xy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_TimeSpent.xy","text":"pars list host species index TimeSpent matrix; string opts list options configure TimeSpent","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.xy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_TimeSpent.xy","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent_athome.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_athome","title":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_athome","text":"Make mosquito dispersal matrix, called TimeSpent","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent_athome.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_athome","text":"","code":"make_TimeSpent_athome(   nPatches,   residence,   opts = list(),   atHome = 1,   travel = 0 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent_athome.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_athome","text":"nPatches number patches residence home patch stratum opts set options overwrites defaults atHome fraction time spent home travel fraction time spent traveling","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent_athome.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_athome","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent_xy.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_xy","title":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_xy","text":"Make mosquito dispersal matrix, called TimeSpent","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent_xy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_xy","text":"","code":"make_TimeSpent_xy(xy, residence, kern, stay, travel)"},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent_xy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_xy","text":"xy xy-locations patches residence home patch stratum kern function gives weight distance stay fraction time spent home travel fraction time spent traveling","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent_xy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_xy","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Make initial values for the SIP human model, with defaults — make_Xinits_SIP","title":"Make initial values for the SIP human model, with defaults — make_Xinits_SIP","text":"Make initial values SIP human model, defaults","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make initial values for the SIP human model, with defaults — make_Xinits_SIP","text":"","code":"make_Xinits_SIP(nStrata, Xopts = list(), H0 = NULL, S0 = NULL, I0 = 1, P0 = 0)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make initial values for the SIP human model, with defaults — make_Xinits_SIP","text":"nStrata number population strata Xopts list overwrite defaults H0 initial human population density S0 initial values parameter S I0 initial values parameter P0 initial values parameter P","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make initial values for the SIP human model, with defaults — make_Xinits_SIP","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Make initial values for the SIS human model, with defaults — make_Xinits_SIS","title":"Make initial values for the SIS human model, with defaults — make_Xinits_SIS","text":"Make initial values SIS human model, defaults","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make initial values for the SIS human model, with defaults — make_Xinits_SIS","text":"","code":"make_Xinits_SIS(nStrata, Xopts = list(), H0 = NULL, S0 = NULL, I0 = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make initial values for the SIS human model, with defaults — make_Xinits_SIS","text":"nStrata number strata model Xopts list overwrite defaults H0 initial human population density S0 initial values parameter S I0 initial values parameter ","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make initial values for the SIS human model, with defaults — make_Xinits_SIS","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for hybrid MoI human model — make_Xinits_hMoI","title":"Make inits for hybrid MoI human model — make_Xinits_hMoI","text":"MoI stands Multiplicity Infection, refers malarial superinfection.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for hybrid MoI human model — make_Xinits_hMoI","text":"","code":"make_Xinits_hMoI(nStrata, Xopts = list(), m10 = 2, m20 = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for hybrid MoI human model — make_Xinits_hMoI","text":"nStrata number population strata Xopts list overwrites default values m10 mean MoI among inapparent human infections m20 mean MoI among patent human infections","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for hybrid MoI human model — make_Xinits_hMoI","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for SIP human model, with defaults — make_Xpar_SIP","title":"Make parameters for SIP human model, with defaults — make_Xpar_SIP","text":"Make parameters SIP human model, defaults","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for SIP human model, with defaults — make_Xpar_SIP","text":"","code":"make_Xpar_SIP(   nStrata,   Xopts = list(),   b = 0.55,   r = 1/180,   c = 0.15,   rho = 0.1,   eta = 1/25,   xi = 1/365 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for SIP human model, with defaults — make_Xpar_SIP","text":"nStrata number population strata Xopts list overwrite defaults b transmission probability (efficiency) mosquito human r recovery rate c transmission probability (efficiency) human mosquito rho probability successful treatment upon infection eta prophylaxis waning rate xi background treatment rate","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for SIP human model, with defaults — make_Xpar_SIP","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for SIS human model, with defaults — make_Xpar_SIS","title":"Make parameters for SIS human model, with defaults — make_Xpar_SIS","text":"Make parameters SIS human model, defaults","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for SIS human model, with defaults — make_Xpar_SIS","text":"","code":"make_Xpar_SIS(nStrata, Xopts = list(), b = 0.55, r = 1/180, c = 0.15)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for SIS human model, with defaults — make_Xpar_SIS","text":"nStrata number population strata Xopts list overwrite defaults b transmission probability (efficiency) mosquito human r recovery rate c transmission probability (efficiency) human mosquito","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for SIS human model, with defaults — make_Xpar_SIS","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for hybrid MoI human model — make_Xpar_hMoI","title":"Make parameters for hybrid MoI human model — make_Xpar_hMoI","text":"MoI stands Multiplicity Infection, refers malarial superinfection.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for hybrid MoI human model — make_Xpar_hMoI","text":"","code":"make_Xpar_hMoI(   nStrata,   Xopts = list(),   b = 0.55,   r1 = 1/180,   r2 = 1/70,   c1 = 0.015,   c2 = 0.15 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for hybrid MoI human model — make_Xpar_hMoI","text":"nStrata number human population strata Xopts list overwrites default values b transmission probability (efficiency) mosquito human r1 recovery rate inapparent infections r2 recovery rate patent infections c1 transmission probability (efficiency) inapparent human infections mosquito c2 transmission probability (efficiency) patent human infections mosquito","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for hybrid MoI human model — make_Xpar_hMoI","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for human null model — make_Xpar_trace","title":"Make parameters for human null model — make_Xpar_trace","text":"Make parameters human null model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for human null model — make_Xpar_trace","text":"","code":"make_Xpar_trace(nPatches, Xopts = list(), kappa = 0.1, Kf = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for human null model — make_Xpar_trace","text":"nPatches number patches model Xopts list overwrite defaults kappa value Kf function","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for human null model — make_Xpar_trace","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.as_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Pass a pre-configured calK — make_calK.as_matrix","title":"Pass a pre-configured calK — make_calK.as_matrix","text":"Implements make_calK as_matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.as_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pass a pre-configured calK — make_calK.as_matrix","text":"","code":"# S3 method for as_matrix make_calK(nPatches, calK, opts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.as_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pass a pre-configured calK — make_calK.as_matrix","text":"nPatches number patches calK matrix string opts list options configure calK","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.as_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pass a pre-configured calK — make_calK.as_matrix","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.herethere.html","id":null,"dir":"Reference","previous_headings":"","what":"Dispersal to every other patch, with equal probability — make_calK.herethere","title":"Dispersal to every other patch, with equal probability — make_calK.herethere","text":"Implements make_calK herethere model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.herethere.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dispersal to every other patch, with equal probability — make_calK.herethere","text":"","code":"# S3 method for herethere make_calK(nPatches, calK = \"herethere\", opts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.herethere.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dispersal to every other patch, with equal probability — make_calK.herethere","text":"nPatches number patches calK matrix string opts list options configure calK","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.herethere.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Dispersal to every other patch, with equal probability — make_calK.herethere","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a mosquito dispersal matrix, called calK — make_calK","title":"Make a mosquito dispersal matrix, called calK — make_calK","text":"Make mosquito dispersal matrix, called calK","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a mosquito dispersal matrix, called calK — make_calK","text":"","code":"make_calK(nPatches, calK, opts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a mosquito dispersal matrix, called calK — make_calK","text":"nPatches number patches calK matrix string opts list options configure calK","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a mosquito dispersal matrix, called calK — make_calK","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.xy.html","id":null,"dir":"Reference","previous_headings":"","what":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK.xy","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK.xy","text":"Implements make_calK kernels","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.xy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK.xy","text":"","code":"# S3 method for xy make_calK(nPatches, calK = \"xy\", opts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.xy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK.xy","text":"nPatches number patches calK matrix string opts list options configure calK","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.xy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK.xy","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK_xy.html","id":null,"dir":"Reference","previous_headings":"","what":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK_xy","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK_xy","text":"Develop mosquito dispersal matrix kernel xy-coordinates","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK_xy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK_xy","text":"","code":"make_calK_xy(xy, ker)"},{"path":"https://dd-harp.github.io/exDE/reference/make_calK_xy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK_xy","text":"xy vector xy-coordinates patch locations ker function weights putative locations distance","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calN.html","id":null,"dir":"Reference","previous_headings":"","what":"Make the habitat membership matrix, calN — make_calN","title":"Make the habitat membership matrix, calN — make_calN","text":"Make habitat membership matrix, calN","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calN.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make the habitat membership matrix, calN — make_calN","text":"","code":"make_calN(nPatches, membership)"},{"path":"https://dd-harp.github.io/exDE/reference/make_calN.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make the habitat membership matrix, calN — make_calN","text":"nPatches number patches membership vector describing patch habitat found","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calN.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make the habitat membership matrix, calN — make_calN","text":"matrix dimensions nPatches nHabitats","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calU.html","id":null,"dir":"Reference","previous_headings":"","what":"Make the egg distribution matrix, calU — make_calU","title":"Make the egg distribution matrix, calU — make_calU","text":"Make egg distribution matrix, calU","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calU.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make the egg distribution matrix, calU — make_calU","text":"","code":"make_calU(calN, searchWts = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/make_calU.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make the egg distribution matrix, calU — make_calU","text":"calN habitat membership matrix searchWts habitat search weights","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calU.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make the egg distribution matrix, calU — make_calU","text":"matrix dimensions nHabitats nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calU_s.html","id":null,"dir":"Reference","previous_headings":"","what":"Make the egg distribution matrix, calU — make_calU_s","title":"Make the egg distribution matrix, calU — make_calU_s","text":"Make egg distribution matrix, calU","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calU_s.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make the egg distribution matrix, calU — make_calU_s","text":"","code":"make_calU_s(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_calU_s.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make the egg distribution matrix, calU — make_calU_s","text":"pars model object s vector species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calU_s.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make the egg distribution matrix, calU — make_calU_s","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices.html","id":null,"dir":"Reference","previous_headings":"","what":"Set indices for generalized spatial model — make_indices","title":"Set indices for generalized spatial model — make_indices","text":"Set indices generalized spatial model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set indices for generalized spatial model — make_indices","text":"","code":"make_indices(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set indices for generalized spatial model — make_indices","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set indices for generalized spatial model — make_indices","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.basic","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.basic","text":"Implements make_indices_L basic competition model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.basic","text":"","code":"# S3 method for basic make_indices_L(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.basic","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.basic","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L","text":"method dispatches type pars$Lpar. Adds field L_ix parameter list.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L","text":"","code":"make_indices_L(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.trace","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.trace","text":"Implements make_indices_L trace (forced emergence) model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.trace","text":"","code":"# S3 method for trace make_indices_L(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.trace","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.trace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.GeRM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_dde","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_dde","text":"Implements make_indices_MYZ GeRM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.GeRM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_dde","text":"","code":"# S3 method for GeRM_dde make_indices_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.GeRM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_dde","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.GeRM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_dde","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.GeRM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_ode","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_ode","text":"Implements make_indices_MYZ GeRM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.GeRM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_ode","text":"","code":"# S3 method for GeRM_ode make_indices_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.GeRM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_ode","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.GeRM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_ode","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.Gtrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_MYZ.Gtrace","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_MYZ.Gtrace","text":"Implements make_indices_MYZ Gtrace (forced emergence) model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.Gtrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_MYZ.Gtrace","text":"","code":"# S3 method for Gtrace make_indices_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.Gtrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_MYZ.Gtrace","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_MYZ.Gtrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.RM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RM_dde","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RM_dde","text":"Implements make_indices_MYZ RM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.RM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RM_dde","text":"","code":"# S3 method for RM_dde make_indices_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.RM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RM_dde","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.RM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RM_dde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.RM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RM_ode","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RM_ode","text":"Implements make_indices_MYZ RM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.RM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RM_ode","text":"","code":"# S3 method for RM_ode make_indices_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.RM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RM_ode","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.RM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RM_ode","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_MYZ.Ztrace","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_MYZ.Ztrace","text":"Implements make_indices_MYZ Ztrace (forced emergence) model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_MYZ.Ztrace","text":"","code":"# S3 method for Ztrace make_indices_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_MYZ.Ztrace","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_MYZ.Ztrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.basicM","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.basicM","text":"Implements make_indices_MYZ basic M model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.basicM","text":"","code":"# S3 method for basicM make_indices_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.basicM","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.basicM","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ","text":"method dispatches type pars$MYZpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ","text":"","code":"make_indices_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for human population to parameter list — make_indices_X.SIP","title":"Add indices for human population to parameter list — make_indices_X.SIP","text":"Implements make_indices_X SIP model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for human population to parameter list — make_indices_X.SIP","text":"","code":"# S3 method for SIP make_indices_X(pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for human population to parameter list — make_indices_X.SIP","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for human population to parameter list — make_indices_X.SIP","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for human population to parameter list — make_indices_X.SIS","title":"Add indices for human population to parameter list — make_indices_X.SIS","text":"Implements make_indices_X SIS model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for human population to parameter list — make_indices_X.SIS","text":"","code":"# S3 method for SIS make_indices_X(pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for human population to parameter list — make_indices_X.SIS","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for human population to parameter list — 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make_parameters_MYZ_Gtrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_MYZ_RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for RM ODE adult mosquito model — make_parameters_MYZ_RM","title":"Make parameters for RM ODE adult mosquito model — make_parameters_MYZ_RM","text":"Make parameters RM ODE adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_MYZ_RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for RM ODE adult mosquito model — make_parameters_MYZ_RM","text":"","code":"make_parameters_MYZ_RM(   pars,   g,   sigma,   f,   q,   nu,   eggsPerBatch,   eip,   calK,   solve_as = \"dde\" )"},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_MYZ_RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for RM ODE adult mosquito model — make_parameters_MYZ_RM","text":"pars list g mosquito mortality rate sigma emigration rate f feeding rate q human blood fraction nu oviposition rate, per mosquito eggsPerBatch eggs laid per oviposition eip length extrinsic incubation period calK mosquito dispersal matrix dimensions nPatches nPatches solve_as either ode solve ode dde solve dde","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_MYZ_RM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for RM ODE adult mosquito model — make_parameters_MYZ_RM","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_MYZ_Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for Ztrace aquatic mosquito model — make_parameters_MYZ_Ztrace","title":"Make parameters for Ztrace aquatic mosquito model — make_parameters_MYZ_Ztrace","text":"Make parameters Ztrace aquatic mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_MYZ_Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for Ztrace aquatic mosquito model — make_parameters_MYZ_Ztrace","text":"","code":"make_parameters_MYZ_Ztrace(pars, Zm, f, q, Zf = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_MYZ_Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for Ztrace aquatic mosquito model — make_parameters_MYZ_Ztrace","text":"pars list Zm vector mean mosquito densities f blood feeding rate q human fraction Zf function form Zf(t, pars) computes temporal fluctuations","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_MYZ_Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for Ztrace aquatic mosquito model — make_parameters_MYZ_Ztrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_MYZ_basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for a basic adult mosquito model — make_parameters_MYZ_basicM","title":"Make parameters for a basic adult mosquito model — make_parameters_MYZ_basicM","text":"Make parameters basic adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_MYZ_basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for a basic adult mosquito model — make_parameters_MYZ_basicM","text":"","code":"make_parameters_MYZ_basicM(pars, g, sigma, f, q, nu, eggsPerBatch, calK)"},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_MYZ_basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for a basic adult mosquito model — make_parameters_MYZ_basicM","text":"pars list g mosquito mortality rate sigma emigration rate f feeding rate q human blood fraction nu oviposition rate, per mosquito eggsPerBatch eggs laid per oviposition calK mosquito dispersal matrix dimensions nPatches nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_MYZ_basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for a basic adult mosquito model — make_parameters_MYZ_basicM","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_X_SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for SIP human model — make_parameters_X_SIP","title":"Make parameters for SIP human model — make_parameters_X_SIP","text":"Make parameters SIP human model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_X_SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for SIP human model — make_parameters_X_SIP","text":"","code":"make_parameters_X_SIP(pars, b, c, r, rho, eta, xi)"},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_X_SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for SIP human model — make_parameters_X_SIP","text":"pars list b transmission probability (efficiency) mosquito human c transmission probability (efficiency) human mosquito r recovery rate rho probability successful treatment upon infection eta prophylaxis waning rate xi background treatment rate","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_X_SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for SIP human model — make_parameters_X_SIP","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_X_SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for SIS human model — make_parameters_X_SIS","title":"Make parameters for SIS human model — make_parameters_X_SIS","text":"Make parameters SIS human model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_X_SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for SIS human model — make_parameters_X_SIS","text":"","code":"make_parameters_X_SIS(pars, b, c, r)"},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_X_SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for SIS human model — make_parameters_X_SIS","text":"pars list b transmission probability (efficiency) mosquito human c transmission probability (efficiency) human mosquito r recovery rate","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_X_SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for SIS human model — make_parameters_X_SIS","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_X_hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for hybrid MoI human model — make_parameters_X_hMoI","title":"Make parameters for hybrid MoI human model — make_parameters_X_hMoI","text":"MoI stands Multiplicity Infection, refers malarial superinfection.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_X_hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for hybrid MoI human model — make_parameters_X_hMoI","text":"","code":"make_parameters_X_hMoI(pars, b, c1, c2, r1, r2)"},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_X_hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for hybrid MoI human model — make_parameters_X_hMoI","text":"pars list b transmission probability (efficiency) mosquito human c1 transmission probability (efficiency) inapparent human infections mosquito c2 transmission probability (efficiency) patent human infections mosquito r1 recovery rate inapparent infections r2 recovery rate patent infections","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_X_hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for hybrid MoI human model — make_parameters_X_hMoI","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_X_trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for trace human model — make_parameters_X_trace","title":"Make parameters for trace human model — make_parameters_X_trace","text":"Make parameters trace human model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_X_trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for trace human model — make_parameters_X_trace","text":"","code":"make_parameters_X_trace(pars, kappa)"},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_X_trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for trace human model — make_parameters_X_trace","text":"pars list kappa net infectiousness","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_X_trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for trace human model — make_parameters_X_trace","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_demography_null.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for null human demography model — make_parameters_demography_null","title":"Make parameters for null human demography model — make_parameters_demography_null","text":"Make parameters null human demography model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_demography_null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for null human demography model — make_parameters_demography_null","text":"","code":"make_parameters_demography_null(pars, H)"},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_demography_null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for null human demography model — make_parameters_demography_null","text":"pars list H size human population strata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_demography_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for null human demography model — make_parameters_demography_null","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_xde.html","id":null,"dir":"Reference","previous_headings":"","what":"Make base parameters, assuming nVectors = nHosts = 1 — make_parameters_xde","title":"Make base parameters, assuming nVectors = nHosts = 1 — make_parameters_xde","text":"Make base parameters, assuming nVectors = nHosts = 1","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_xde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make base parameters, assuming nVectors = nHosts = 1 — make_parameters_xde","text":"","code":"make_parameters_xde(solve_as = \"dde\")"},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_xde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make base parameters, assuming nVectors = nHosts = 1 — make_parameters_xde","text":"solve_as, either \"ode\" \"dde\"","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_xde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make base parameters, assuming nVectors = nHosts = 1 — make_parameters_xde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calD.html","id":null,"dir":"Reference","previous_headings":"","what":"Parasite dispersal by humans — metric_calD","title":"Parasite dispersal by humans — metric_calD","text":"Compute p p matrix \\(\\mathcal{D}\\) whose columns describe potentially infectious person time persons patch dispersed across patches. $$\\mathcal{D} = \\mbox{diag}\\left(W \\right) \\cdot \\beta^T \\cdot \\mbox{diag}\\left(bDH\\right) \\cdot \\beta$$","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calD.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parasite dispersal by humans — metric_calD","text":"","code":"metric_calD(W, beta, b, D, H)"},{"path":"https://dd-harp.github.io/exDE/reference/metric_calD.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parasite dispersal by humans — metric_calD","text":"W ambient human population patch beta biting distribution matrix b transmission efficiency mosquitoes humans D human transmitting capacity H human population size strata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calD.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parasite dispersal by humans — metric_calD","text":"numeric matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calR.html","id":null,"dir":"Reference","previous_headings":"","what":"Parasite Dispersal through one Parasite Generation (Humans) — metric_calR","title":"Parasite Dispersal through one Parasite Generation (Humans) — metric_calR","text":"Computes n n matrix describing parasite dispersal infecteds (columns) infectees (rows). $$\\mathcal{R} =   b \\beta \\cdot {\\cal V}  \\cdot \\mbox{diag}\\left(W \\right) \\cdot \\beta^T  \\cdot \\mbox{diag}\\left(DH\\right)$$","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parasite Dispersal through one Parasite Generation (Humans) — metric_calR","text":"","code":"metric_calR(b, beta, calV, W, D, H)"},{"path":"https://dd-harp.github.io/exDE/reference/metric_calR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parasite Dispersal through one Parasite Generation (Humans) — metric_calR","text":"b transmission efficiency mosquitoes humans beta biting distribution matrix calV parasite dispersal mosquitoes matrix (see metric_calV) W ambient human population patch D human transmitting capacity H human population size strata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parasite Dispersal through one Parasite Generation (Humans) — metric_calR","text":"numeric matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calV.html","id":null,"dir":"Reference","previous_headings":"","what":"Parasite dispersal by mosquitoes — metric_calV","title":"Parasite dispersal by mosquitoes — metric_calV","text":"Compute p p matrix \\(\\mathcal{V}\\) whose columns describe infective bites arising mosquitoes biting single human single day dispersed patches, accounting movement mortality. $$\\mathcal{V} = fq\\Omega^{-1} \\cdot e^{-\\Omega\\tau} \\cdot \\mbox{diag}\\left(\\frac{fqM}{W}\\right)$$","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calV.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parasite dispersal by mosquitoes — metric_calV","text":"","code":"metric_calV(f, q, Omega, tau, M, W)"},{"path":"https://dd-harp.github.io/exDE/reference/metric_calV.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parasite dispersal by mosquitoes — metric_calV","text":"f feeding rate q fraction bloodmeals taken humans Omega mosquito demography matrix tau duration extrinsic incubation period M size mosquito population patch W ambient human population patch","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calV.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parasite dispersal by mosquitoes — metric_calV","text":"numeric matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Parasite Dispersal through one Parasite Generation (Mosquitoes) — metric_calZ","title":"Parasite Dispersal through one Parasite Generation (Mosquitoes) — metric_calZ","text":"Computes p p matrix describing parasite dispersal infecteds (columns) infectees (rows). $$\\mathcal{Z} = e^{-\\Omega\\tau} \\cdot \\mbox{diag}\\left( \\frac{fq M}{W} \\right) \\cdot {\\cal D} \\cdot  fq\\Omega^{-1}$$","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parasite Dispersal through one Parasite Generation (Mosquitoes) — metric_calZ","text":"","code":"metric_calZ(Omega, tau, f, q, M, W, calD)"},{"path":"https://dd-harp.github.io/exDE/reference/metric_calZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parasite Dispersal through one Parasite Generation (Mosquitoes) — metric_calZ","text":"Omega mosquito demography matrix tau duration extrinsic incubation period f feeding rate q fraction bloodmeals taken humans M size mosquito population patch W ambient human population patch calD parasite dispersal humans matrix (see metric_calD)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calZ.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parasite Dispersal through one Parasite Generation (Mosquitoes) — metric_calZ","text":"numeric matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of an object returned by deSolve — parse_deout","title":"Parse the output of an object returned by deSolve — parse_deout","text":"Parse output object returned deSolve","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of an object returned by deSolve — parse_deout","text":"","code":"parse_deout(deout, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of an object returned by deSolve — parse_deout","text":"deout matrix orbits returned deSolve pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of an object returned by deSolve — parse_deout","text":"varslist list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the variable names for the basic model — parse_deout_L.basic","title":"Parse the variable names for the basic model — parse_deout_L.basic","text":"Implements parse_deout_L basic competition model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the variable names for the basic model — parse_deout_L.basic","text":"","code":"# S3 method for basic parse_deout_L(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the variable names for the basic model — parse_deout_L.basic","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the variable names for the basic model — parse_deout_L.basic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return the variables by name in a list — parse_deout_L","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_L","text":"method dispatches type pars$Lpar. Attaches state variables aquatic ecology model list returns ","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_L","text":"","code":"parse_deout_L(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_L","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the variable names for the trace model — parse_deout_L.trace","title":"Parse the variable names for the trace model — parse_deout_L.trace","text":"Implements parse_deout_L trace model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the variable names for the trace model — parse_deout_L.trace","text":"","code":"# S3 method for trace parse_deout_L(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the variable names for the trace model — parse_deout_L.trace","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the variable names for the trace model — parse_deout_L.trace","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.GeRM.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the GeRM model — parse_deout_MYZ.GeRM","title":"Parse the output of deSolve and return variables for the GeRM model — parse_deout_MYZ.GeRM","text":"Implements parse_deout_MYZ GeRM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.GeRM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the GeRM model — parse_deout_MYZ.GeRM","text":"","code":"# S3 method for GeRM parse_deout_MYZ(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.GeRM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the GeRM model — parse_deout_MYZ.GeRM","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.GeRM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the GeRM model — parse_deout_MYZ.GeRM","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.Gtrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the Gtrace model — parse_deout_MYZ.Gtrace","title":"Parse the output of deSolve and return variables for the Gtrace model — parse_deout_MYZ.Gtrace","text":"Implements parse_deout_MYZ Gtrace","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.Gtrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the Gtrace model — parse_deout_MYZ.Gtrace","text":"","code":"# S3 method for Gtrace parse_deout_MYZ(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.Gtrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the Gtrace model — parse_deout_MYZ.Gtrace","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the Gtrace model — parse_deout_MYZ.Gtrace","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the RM model — parse_deout_MYZ.RM","title":"Parse the output of deSolve and return variables for the RM model — parse_deout_MYZ.RM","text":"Implements parse_deout_MYZ RM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the RM model — parse_deout_MYZ.RM","text":"","code":"# S3 method for RM parse_deout_MYZ(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the RM model — parse_deout_MYZ.RM","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.RM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the RM model — parse_deout_MYZ.RM","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the Ztrace model — parse_deout_MYZ.Ztrace","title":"Parse the output of deSolve and return variables for the Ztrace model — parse_deout_MYZ.Ztrace","text":"Implements parse_deout_MYZ Ztrace","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the Ztrace model — parse_deout_MYZ.Ztrace","text":"","code":"# S3 method for Ztrace parse_deout_MYZ(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the Ztrace model — parse_deout_MYZ.Ztrace","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the Ztrace model — parse_deout_MYZ.Ztrace","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the basicM model — parse_deout_MYZ.basicM","title":"Parse the output of deSolve and return variables for the basicM model — parse_deout_MYZ.basicM","text":"Implements parse_deout_MYZ basicM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the basicM model — parse_deout_MYZ.basicM","text":"","code":"# S3 method for basicM parse_deout_MYZ(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the basicM model — parse_deout_MYZ.basicM","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the basicM model — parse_deout_MYZ.basicM","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return the variables by name in a list — parse_deout_MYZ","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_MYZ","text":"method dispatches type pars$MYZpar. computes variables name returns named list.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_MYZ","text":"","code":"parse_deout_MYZ(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_MYZ","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_MYZ","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the SIP model — parse_deout_X.SIP","title":"Parse the output of deSolve and return variables for the SIP model — parse_deout_X.SIP","text":"Implements parse_deout_X SIP model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the SIP model — parse_deout_X.SIP","text":"","code":"# S3 method for SIP parse_deout_X(deout, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the SIP model — parse_deout_X.SIP","text":"deout matrix outputs deSolve pars list defines model host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the SIP model — parse_deout_X.SIP","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the SIS model — parse_deout_X.SIS","title":"Parse the output of deSolve and return variables for the SIS model — parse_deout_X.SIS","text":"Implements parse_deout_X SIS model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the SIS model — parse_deout_X.SIS","text":"","code":"# S3 method for SIS parse_deout_X(deout, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the SIS model — parse_deout_X.SIS","text":"deout matrix outputs deSolve pars list defines model host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the SIS model — parse_deout_X.SIS","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the hMoI model — parse_deout_X.hMoI","title":"Parse the output of deSolve and return variables for the hMoI model — parse_deout_X.hMoI","text":"Implements parse_deout_X hMoI model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the hMoI model — parse_deout_X.hMoI","text":"","code":"# S3 method for hMoI parse_deout_X(deout, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the hMoI model — parse_deout_X.hMoI","text":"deout matrix outputs deSolve pars list defines model host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the hMoI model — parse_deout_X.hMoI","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return the variables by name in a list — parse_deout_X","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_X","text":"method dispatches type pars$Xpar. Adds variables X model list returns ","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_X","text":"","code":"parse_deout_X(deout, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_X","text":"deout matrix outputs deSolve pars list defines model host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the trace model — parse_deout_X.trace","title":"Parse the output of deSolve and return variables for the trace model — parse_deout_X.trace","text":"Implements parse_deout_X trace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the trace model — parse_deout_X.trace","text":"","code":"# S3 method for trace parse_deout_X(deout, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the trace model — parse_deout_X.trace","text":"deout matrix outputs deSolve pars list defines model host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the trace model — parse_deout_X.trace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_vec.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of an object returned by deSolve — parse_deout_vec","title":"Parse the output of an object returned by deSolve — parse_deout_vec","text":"Parse output object returned deSolve","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_vec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of an object returned by deSolve — parse_deout_vec","text":"","code":"parse_deout_vec(vec, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_vec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of an object returned by deSolve — parse_deout_vec","text":"vec vector variables, returned rootsolve pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_vec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of an object returned by deSolve — parse_deout_vec","text":"varslist list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_BFpar_static.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the blood feeding model — setup_BFpar_static","title":"Set up the blood feeding model — setup_BFpar_static","text":"sets list stores information required blood feeding model, including information humans (residence vector, search weights blood feeding mosquitoes); mosquitoes circadian pattern (F_circadian); derived structures, including time spent (TimeSpent) time risk (TaR) matrices. also sets objects required blood feeding, including host availability species (Wi) hosts (W), blood hosts (), total blood availability (B). Finally, sets lists hold mixing matrix (beta), transmission terms describing entomological inoculation rate (EIR eir), force infection (FoI), net infectiousness (kappa ni).","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_BFpar_static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the blood feeding model — setup_BFpar_static","text":"","code":"setup_BFpar_static(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_BFpar_static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the blood feeding model — setup_BFpar_static","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_BFpar_static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the blood feeding model — setup_BFpar_static","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_BloodFeeding.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up blood feeding — setup_BloodFeeding","title":"Set up blood feeding — setup_BloodFeeding","text":"sets list stores information","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_BloodFeeding.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up blood feeding — setup_BloodFeeding","text":"","code":"setup_BloodFeeding(   pars,   i,   s = 1,   BFopts = list(),   residence = 1,   searchWts = 1,   F_circadian = NULL )"},{"path":"https://dd-harp.github.io/exDE/reference/setup_BloodFeeding.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up blood feeding — setup_BloodFeeding","text":"pars list host species index s vector species index BFopts list residence patch stratum resides searchWts blood feeding search weight stratum F_circadian function computes relative mosquito blood feeding activity rates time day","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_BloodFeeding.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up blood feeding — setup_BloodFeeding","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EGGpar_static.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the structures required for egg laying — setup_EGGpar_static","title":"Setup the structures required for egg laying — setup_EGGpar_static","text":"sets object EGGpar, holds information egg laying model. Several terms expected differ vector species, including search weights (searchWts), fraction eggs laid habitat sometimes suitable (Qfrac), egg deposition matrix (calU), habitat egg laying rate (eggs_laid). function sets lists.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EGGpar_static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the structures required for egg laying — setup_EGGpar_static","text":"","code":"setup_EGGpar_static(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_EGGpar_static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the structures required for egg laying — setup_EGGpar_static","text":"pars model object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EGGpar_static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the structures required for egg laying — setup_EGGpar_static","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the static model for control forcing (do nothing) — setup_EIP","title":"Set up the static model for control forcing (do nothing) — setup_EIP","text":"Set static model control forcing (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the static model for control forcing (do nothing) — setup_EIP","text":"","code":"setup_EIP(EIPname = \"static\", EIPopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_EIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the static model for control forcing (do nothing) — setup_EIP","text":"EIPname class name function EIPopts list overwrites default options","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the static model for control forcing (do nothing) — setup_EIP","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EIP.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up a static model for the EIP — setup_EIP.static","title":"Set up a static model for the EIP — setup_EIP.static","text":"Set static model EIP","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EIP.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up a static model for the EIP — setup_EIP.static","text":"","code":"# S3 method for static setup_EIP(EIPname, EIPopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_EIP.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up a static model for the EIP — setup_EIP.static","text":"EIPname class name function EIPopts list overwrites default options","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EIP.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up a static model for the EIP — setup_EIP.static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EggLaying_simple.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup egg laying for most models — setup_EggLaying_simple","title":"Setup egg laying for most models — setup_EggLaying_simple","text":"Sets egg-deposition matrix calU s^th species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EggLaying_simple.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup egg laying for most models — setup_EggLaying_simple","text":"","code":"setup_EggLaying_simple(pars, s, searchQ = 1, Lopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_EggLaying_simple.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup egg laying for most models — setup_EggLaying_simple","text":"pars model object s vector species index searchQ membership matrix Lopts list options override defaults","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EggLaying_simple.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup egg laying for most models — setup_EggLaying_simple","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EggLaying_static.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup egg laying for most models — setup_EggLaying_static","title":"Setup egg laying for most models — setup_EggLaying_static","text":"Sets egg-deposition matrix calU s^th species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EggLaying_static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup egg laying for most models — setup_EggLaying_static","text":"","code":"setup_EggLaying_static(pars, s, searchQ = 1, Lopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_EggLaying_static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup egg laying for most models — setup_EggLaying_static","text":"pars model object s vector species index searchQ membership matrix Lopts list options override defaults","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EggLaying_static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup egg laying for most models — setup_EggLaying_static","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Hpar_static.html","id":null,"dir":"Reference","previous_headings":"","what":"A utility to set up Hpar — setup_Hpar_static","title":"A utility to set up Hpar — setup_Hpar_static","text":"utility set Hpar","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Hpar_static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A utility to set up Hpar — setup_Hpar_static","text":"","code":"setup_Hpar_static(pars, i, HPop = 1000)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Hpar_static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A utility to set up Hpar — setup_Hpar_static","text":"pars list host species index HPop numeric vector population densities","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Hpar_static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A utility to set up Hpar — setup_Hpar_static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the basic model — setup_Linits.basic","title":"Setup the basic model — setup_Linits.basic","text":"Implements setup_Linits basic model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the basic model — setup_Linits.basic","text":"","code":"# S3 method for basic setup_Linits(pars, s, Lopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the basic model — setup_Linits.basic","text":"pars list s species index Lopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the basic model — setup_Linits.basic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to set up adult mosquito models — setup_Linits","title":"A function to set up adult mosquito models — setup_Linits","text":"method dispatches Lname.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to set up adult mosquito models — setup_Linits","text":"","code":"setup_Linits(pars, s, Lopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to set up adult mosquito models — setup_Linits","text":"pars list s species index Lopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to set up adult mosquito models — setup_Linits","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the trace model — setup_Linits.trace","title":"Setup the trace model — setup_Linits.trace","text":"Implements setup_Linits trace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the trace model — setup_Linits.trace","text":"","code":"# S3 method for trace setup_Linits(pars, s, Lopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the trace model — setup_Linits.trace","text":"pars list s species index Lopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the trace model — setup_Linits.trace","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Lpar for the basic model — setup_Lpar.basic","title":"Setup Lpar for the basic model — setup_Lpar.basic","text":"Implements setup_Lpar basic model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Lpar for the basic model — setup_Lpar.basic","text":"","code":"# S3 method for basic setup_Lpar(Lname, pars, s, Lopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Lpar for the basic model — setup_Lpar.basic","text":"Lname class name aquatic model pars list s species index Lopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Lpar for the basic model — setup_Lpar.basic","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to set up adult mosquito models — setup_Lpar","title":"A function to set up adult mosquito models — setup_Lpar","text":"method dispatches Lname.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to set up adult mosquito models — setup_Lpar","text":"","code":"setup_Lpar(Lname, pars, s, Lopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to set up adult mosquito models — setup_Lpar","text":"Lname class name aquatic model pars list s species index Lopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to set up adult mosquito models — setup_Lpar","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Lpar for the trace model — setup_Lpar.trace","title":"Setup Lpar for the trace model — setup_Lpar.trace","text":"Implements setup_Lpar trace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Lpar for the trace model — setup_Lpar.trace","text":"","code":"# S3 method for trace setup_Lpar(Lname, pars, s, Lopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Lpar for the trace model — setup_Lpar.trace","text":"Lname class name aquatic model pars list s species index Lopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Lpar for the trace model — setup_Lpar.trace","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.GeRM.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the GeRM model — setup_MYZinits.GeRM","title":"Setup the GeRM model — setup_MYZinits.GeRM","text":"Implements setup_MYZinits GeRM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.GeRM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the GeRM model — setup_MYZinits.GeRM","text":"","code":"# S3 method for GeRM setup_MYZinits(pars, s, MYZopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.GeRM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the GeRM model — setup_MYZinits.GeRM","text":"pars list s species index MYZopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.GeRM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the GeRM model — setup_MYZinits.GeRM","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.Gtrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the Gtrace model — setup_MYZinits.Gtrace","title":"Setup the Gtrace model — setup_MYZinits.Gtrace","text":"Implements setup_MYZinits Gtrace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.Gtrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the Gtrace model — setup_MYZinits.Gtrace","text":"","code":"# S3 method for Gtrace setup_MYZinits(pars, s, MYZopts = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.Gtrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the Gtrace model — setup_MYZinits.Gtrace","text":"pars list s species index MYZopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the Gtrace model — setup_MYZinits.Gtrace","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup initial values for the RM model — setup_MYZinits.RM","title":"Setup initial values for the RM model — setup_MYZinits.RM","text":"Implements setup_MYZinits RM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup initial values for the RM model — setup_MYZinits.RM","text":"","code":"# S3 method for RM setup_MYZinits(pars, s, MYZopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup initial values for the RM model — setup_MYZinits.RM","text":"pars list s species index MYZopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.RM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup initial values for the RM model — setup_MYZinits.RM","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the Ztrace model — setup_MYZinits.Ztrace","title":"Setup the Ztrace model — setup_MYZinits.Ztrace","text":"Implements setup_MYZinits Ztrace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the Ztrace model — setup_MYZinits.Ztrace","text":"","code":"# S3 method for Ztrace setup_MYZinits(pars, s, MYZopts = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the Ztrace model — setup_MYZinits.Ztrace","text":"pars list s species index MYZopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the Ztrace model — setup_MYZinits.Ztrace","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the basicM model — setup_MYZinits.basicM","title":"Setup the basicM model — setup_MYZinits.basicM","text":"Implements setup_MYZinits basicM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the basicM model — setup_MYZinits.basicM","text":"","code":"# S3 method for basicM setup_MYZinits(pars, s, MYZopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the basicM model — setup_MYZinits.basicM","text":"pars list s species index MYZopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the basicM model — setup_MYZinits.basicM","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to set up adult mosquito models — setup_MYZinits","title":"A function to set up adult mosquito models — setup_MYZinits","text":"method dispatches MYZname.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to set up adult mosquito models — setup_MYZinits","text":"","code":"setup_MYZinits(pars, s, MYZopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to set up adult mosquito models — setup_MYZinits","text":"pars list s species index MYZopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to set up adult mosquito models — setup_MYZinits","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.GeRM.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup MYZpar for the GeRM model — setup_MYZpar.GeRM","title":"Setup MYZpar for the GeRM model — setup_MYZpar.GeRM","text":"Implements setup_MYZpar GeRM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.GeRM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup MYZpar for the GeRM model — setup_MYZpar.GeRM","text":"","code":"# S3 method for GeRM setup_MYZpar(MYZname, pars, s, MYZopts = list(), EIPmod, calK)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.GeRM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup MYZpar for the GeRM model — setup_MYZpar.GeRM","text":"MYZname name model pars list s species index MYZopts list EIPmod list calK matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.GeRM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup MYZpar for the GeRM model — setup_MYZpar.GeRM","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.Gtrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the Gtrace — setup_MYZpar.Gtrace","title":"Setup the Gtrace — setup_MYZpar.Gtrace","text":"Implements setup_MYZpar Gtrace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.Gtrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the Gtrace — setup_MYZpar.Gtrace","text":"","code":"# S3 method for Gtrace setup_MYZpar(MYZname, pars, s, MYZopts = NULL, EIPmod = NULL, calK = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.Gtrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the Gtrace — setup_MYZpar.Gtrace","text":"MYZname name model pars list s species index MYZopts list EIPmod list calK matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the Gtrace — setup_MYZpar.Gtrace","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup MYZpar for the RM model — setup_MYZpar.RM","title":"Setup MYZpar for the RM model — setup_MYZpar.RM","text":"Implements setup_MYZpar RM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup MYZpar for the RM model — setup_MYZpar.RM","text":"","code":"# S3 method for RM setup_MYZpar(MYZname, pars, s, MYZopts = list(), EIPmod, calK)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup MYZpar for the RM model — setup_MYZpar.RM","text":"MYZname name model pars list s species index MYZopts list EIPmod list calK matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.RM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup MYZpar for the RM model — setup_MYZpar.RM","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the Ztrace model — setup_MYZpar.Ztrace","title":"Setup the Ztrace model — setup_MYZpar.Ztrace","text":"Implements setup_MYZpar Ztrace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the Ztrace model — setup_MYZpar.Ztrace","text":"","code":"# S3 method for Ztrace setup_MYZpar(MYZname, pars, s, MYZopts = NULL, EIPmod = NULL, calK = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the Ztrace model — setup_MYZpar.Ztrace","text":"MYZname name model pars list s species index MYZopts list EIPmod list calK matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the Ztrace model — setup_MYZpar.Ztrace","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup MYZpar for the basicM model — setup_MYZpar.basicM","title":"Setup MYZpar for the basicM model — setup_MYZpar.basicM","text":"Implements setup_MYZpar basicM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup MYZpar for the basicM model — setup_MYZpar.basicM","text":"","code":"# S3 method for basicM setup_MYZpar(MYZname, pars, s, MYZopts = list(), EIPmod = NULL, calK)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup MYZpar for the basicM model — setup_MYZpar.basicM","text":"MYZname name model pars list s species index MYZopts list EIPmod list calK matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup MYZpar for the basicM model — setup_MYZpar.basicM","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to set up adult mosquito models — setup_MYZpar","title":"A function to set up adult mosquito models — setup_MYZpar","text":"method dispatches MYZname.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to set up adult mosquito models — setup_MYZpar","text":"","code":"setup_MYZpar(   MYZname,   pars,   s,   MYZopts = list(),   EIPmod = setup_eip_static(),   calK = diag(1) )"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to set up adult mosquito models — setup_MYZpar","text":"MYZname name model pars list s species index MYZopts list EIPmod list calK matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to set up adult mosquito models — setup_MYZpar","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xinits.SIP — setup_Xinits.SIP","title":"Setup Xinits.SIP — setup_Xinits.SIP","text":"Implements setup_Xinits SIP model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xinits.SIP — setup_Xinits.SIP","text":"","code":"# S3 method for SIP setup_Xinits(pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xinits.SIP — setup_Xinits.SIP","text":"pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xinits.SIP — setup_Xinits.SIP","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xinits.SIS — setup_Xinits.SIS","title":"Setup Xinits.SIS — setup_Xinits.SIS","text":"Implements setup_Xinits SIS model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xinits.SIS — setup_Xinits.SIS","text":"","code":"# S3 method for SIS setup_Xinits(pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xinits.SIS — setup_Xinits.SIS","text":"pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xinits.SIS — setup_Xinits.SIS","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xinits.hMoI — setup_Xinits.hMoI","title":"Setup Xinits.hMoI — setup_Xinits.hMoI","text":"Implements setup_Xinits hMoI model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xinits.hMoI — setup_Xinits.hMoI","text":"","code":"# S3 method for hMoI setup_Xinits(pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xinits.hMoI — setup_Xinits.hMoI","text":"pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xinits.hMoI — setup_Xinits.hMoI","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to set up Xpar — setup_Xinits","title":"A function to set up Xpar — setup_Xinits","text":"method dispatches Xname.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to set up Xpar — setup_Xinits","text":"","code":"setup_Xinits(pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to set up Xpar — setup_Xinits","text":"pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to set up Xpar — setup_Xinits","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xinits.trace — setup_Xinits.trace","title":"Setup Xinits.trace — setup_Xinits.trace","text":"Implements setup_Xinits trace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xinits.trace — setup_Xinits.trace","text":"","code":"# S3 method for trace setup_Xinits(pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xinits.trace — setup_Xinits.trace","text":"pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xinits.trace — setup_Xinits.trace","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xpar.SIP — setup_Xpar.SIP","title":"Setup Xpar.SIP — setup_Xpar.SIP","text":"Implements setup_Xpar SIP model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xpar.SIP — setup_Xpar.SIP","text":"","code":"# S3 method for SIP setup_Xpar(Xname, pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xpar.SIP — setup_Xpar.SIP","text":"Xname character string pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xpar.SIP — setup_Xpar.SIP","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xpar.SIS — setup_Xpar.SIS","title":"Setup Xpar.SIS — setup_Xpar.SIS","text":"Implements setup_Xpar SIS model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xpar.SIS — setup_Xpar.SIS","text":"","code":"# S3 method for SIS setup_Xpar(Xname, pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xpar.SIS — setup_Xpar.SIS","text":"Xname character string pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xpar.SIS — setup_Xpar.SIS","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xpar.hMoI — setup_Xpar.hMoI","title":"Setup Xpar.hMoI — setup_Xpar.hMoI","text":"Implements setup_Xpar hMoI model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xpar.hMoI — setup_Xpar.hMoI","text":"","code":"# S3 method for hMoI setup_Xpar(Xname, pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xpar.hMoI — setup_Xpar.hMoI","text":"Xname character string pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xpar.hMoI — setup_Xpar.hMoI","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to set up Xpar — setup_Xpar","title":"A function to set up Xpar — setup_Xpar","text":"method dispatches Xname.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to set up Xpar — setup_Xpar","text":"","code":"setup_Xpar(Xname, pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to set up Xpar — setup_Xpar","text":"Xname character string pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to set up Xpar — setup_Xpar","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xpar.trace — setup_Xpar.trace","title":"Setup Xpar.trace — setup_Xpar.trace","text":"Implements setup_Xpar trace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xpar.trace — setup_Xpar.trace","text":"","code":"# S3 method for trace setup_Xpar(Xname, pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xpar.trace — setup_Xpar.trace","text":"Xname character string pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xpar.trace — setup_Xpar.trace","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_abiotic_forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for the null model of abiotic forcing (do nothing) — setup_abiotic_forced","title":"Make parameters for the null model of abiotic forcing (do nothing) — setup_abiotic_forced","text":"Make parameters null model abiotic forcing (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_abiotic_forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for the null model of abiotic forcing (do nothing) — setup_abiotic_forced","text":"","code":"setup_abiotic_forced(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_abiotic_forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for the null model of abiotic forcing (do nothing) — setup_abiotic_forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_abiotic_forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for the null model of abiotic forcing (do nothing) — setup_abiotic_forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_abiotic_null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the null model for exogenous forcing (do nothing) — setup_abiotic_null","title":"Set up the null model for exogenous forcing (do nothing) — setup_abiotic_null","text":"Set null model exogenous forcing (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_abiotic_null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the null model for exogenous forcing (do nothing) — setup_abiotic_null","text":"","code":"setup_abiotic_null(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_abiotic_null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the null model for exogenous forcing (do nothing) — setup_abiotic_null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_abiotic_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the null model for exogenous forcing (do nothing) — setup_abiotic_null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_area_spray_null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the null model for area spraying (do nothing) — setup_area_spray_null","title":"Set up the null model for area spraying (do nothing) — setup_area_spray_null","text":"Set null model area spraying (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_area_spray_null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the null model for area spraying (do nothing) — setup_area_spray_null","text":"","code":"setup_area_spray_null(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_area_spray_null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the null model for area spraying (do nothing) — setup_area_spray_null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_area_spray_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the null model for area spraying (do nothing) — setup_area_spray_null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup behavior — setup_behavior.forced","title":"Setup behavior — setup_behavior.forced","text":"Setup behavior","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup behavior — setup_behavior.forced","text":"","code":"# S3 method for forced setup_behavior(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup behavior — setup_behavior.forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup behavior — setup_behavior.forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup behavior — setup_behavior","title":"Setup behavior — setup_behavior","text":"Setup behavior","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup behavior — setup_behavior","text":"","code":"setup_behavior(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup behavior — setup_behavior","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup behavior — setup_behavior","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup behavior — setup_behavior.null","title":"Setup behavior — setup_behavior.null","text":"Setup behavior","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup behavior — setup_behavior.null","text":"","code":"# S3 method for null setup_behavior(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup behavior — setup_behavior.null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup behavior — setup_behavior.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior_forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for the forced model for resource availability (do nothing) — setup_behavior_forced","title":"Make parameters for the forced model for resource availability (do nothing) — setup_behavior_forced","text":"Make parameters forced model resource availability (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior_forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for the forced model for resource availability (do nothing) — setup_behavior_forced","text":"","code":"setup_behavior_forced(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior_forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for the forced model for resource availability (do nothing) — setup_behavior_forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior_forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for the forced model for resource availability (do nothing) — setup_behavior_forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior_null.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for the null model for resource availability (do nothing) — setup_behavior_null","title":"Make parameters for the null model for resource availability (do nothing) — setup_behavior_null","text":"Make parameters null model resource availability (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior_null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for the null model for resource availability (do nothing) — setup_behavior_null","text":"","code":"setup_behavior_null(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior_null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for the null model for resource availability (do nothing) — setup_behavior_null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for the null model for resource availability (do nothing) — setup_behavior_null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_bionomics_static.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for the static model bionomics — setup_bionomics_static","title":"Make parameters for the static model bionomics — setup_bionomics_static","text":"Make parameters static model bionomics","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_bionomics_static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for the static model bionomics — setup_bionomics_static","text":"","code":"setup_bionomics_static(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_bionomics_static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for the static model bionomics — setup_bionomics_static","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_bionomics_static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for the static model bionomics — setup_bionomics_static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_care_seeking_null.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for the null model for care seeking (do nothing) — setup_care_seeking_null","title":"Make parameters for the null model for care seeking (do nothing) — setup_care_seeking_null","text":"Make parameters null model care seeking (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_care_seeking_null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for the null model for care seeking (do nothing) — setup_care_seeking_null","text":"","code":"setup_care_seeking_null(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_care_seeking_null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for the null model for care seeking (do nothing) — setup_care_seeking_null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_care_seeking_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for the null model for care seeking (do nothing) — setup_care_seeking_null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_civil_forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for the null model of civil forcing (do nothing) — setup_civil_forced","title":"Make parameters for the null model of civil forcing (do nothing) — setup_civil_forced","text":"Make parameters null model civil forcing (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_civil_forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for the null model of civil forcing (do nothing) — setup_civil_forced","text":"","code":"setup_civil_forced(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_civil_forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for the null model of civil forcing (do nothing) — setup_civil_forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_civil_forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for the null model of civil forcing (do nothing) — setup_civil_forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_civil_null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the null model for exogenous forcing (do nothing) — setup_civil_null","title":"Set up the null model for exogenous forcing (do nothing) — setup_civil_null","text":"Set null model exogenous forcing (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_civil_null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the null model for exogenous forcing (do nothing) — setup_civil_null","text":"","code":"setup_civil_null(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_civil_null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the null model for exogenous forcing (do nothing) — setup_civil_null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_civil_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the null model for exogenous forcing (do nothing) — setup_civil_null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_clinic_forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up a model for clinic — setup_clinic_forced","title":"Set up a model for clinic — setup_clinic_forced","text":"Set model clinic","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_clinic_forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up a model for clinic — setup_clinic_forced","text":"","code":"setup_clinic_forced(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_clinic_forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up a model for clinic — setup_clinic_forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_clinic_forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up a model for clinic — setup_clinic_forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_clinic_null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the null model for clinical distribution (do nothing) — setup_clinic_null","title":"Set up the null model for clinical distribution (do nothing) — setup_clinic_null","text":"Set null model clinical distribution (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_clinic_null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the null model for clinical distribution (do nothing) — setup_clinic_null","text":"","code":"setup_clinic_null(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_clinic_null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the null model for clinical distribution (do nothing) — setup_clinic_null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_clinic_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the null model for clinical distribution (do nothing) — setup_clinic_null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_control.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup control — setup_control.forced","title":"Setup control — setup_control.forced","text":"Setup control","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_control.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup control — setup_control.forced","text":"","code":"# S3 method for forced setup_control(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_control.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup control — setup_control.forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_control.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup control — setup_control.forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_control.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup CONTROL with forcing — setup_control","title":"Setup CONTROL with forcing — setup_control","text":"Setup CONTROL forcing","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup CONTROL with forcing — setup_control","text":"","code":"setup_control(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup CONTROL with forcing — setup_control","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_control.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup CONTROL with forcing — setup_control","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_control.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup control — setup_control.null","title":"Setup control — setup_control.null","text":"Setup control","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_control.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup control — setup_control.null","text":"","code":"# S3 method for null setup_control(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_control.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup control — setup_control.null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_control.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup control — setup_control.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_control_forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up a model with some control — setup_control_forced","title":"Set up a model with some control — setup_control_forced","text":"Set model control","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_control_forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up a model with some control — setup_control_forced","text":"","code":"setup_control_forced(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_control_forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up a model with some control — setup_control_forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_control_forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up a model with some control — setup_control_forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_control_null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the null model for control forcing (do nothing) — setup_control_null","title":"Set up the null model for control forcing (do nothing) — setup_control_null","text":"Set null model control forcing (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_control_null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the null model for control forcing (do nothing) — setup_control_null","text":"","code":"setup_control_null(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_control_null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the null model for control forcing (do nothing) — setup_control_null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_control_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the null model for control forcing (do nothing) — setup_control_null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_development_null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the null model for developments (do nothing) — setup_development_null","title":"Set up the null model for developments (do nothing) — setup_development_null","text":"Set null model developments (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_development_null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the null model for developments (do nothing) — setup_development_null","text":"","code":"setup_development_null(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_development_null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the null model for developments (do nothing) — setup_development_null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_development_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the null model for developments (do nothing) — setup_development_null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_eip_static.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up a static model for 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static model for sugar (do nothing) — setup_sugar_static","title":"Make parameters for the static model for sugar (do nothing) — setup_sugar_static","text":"Make parameters static model sugar (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_sugar_static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for the static model for sugar (do nothing) — setup_sugar_static","text":"","code":"setup_sugar_static(pars, Sugar = 0)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_sugar_static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for the static model for sugar (do nothing) — setup_sugar_static","text":"pars list Sugar describes sugar availability","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_sugar_static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for the static model for sugar (do nothing) — setup_sugar_static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_temperature_null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the null model for temperature — setup_temperature_null","title":"Set up the null model for temperature — setup_temperature_null","text":"Set null model temperature","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_temperature_null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the null model for temperature — setup_temperature_null","text":"","code":"setup_temperature_null(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_temperature_null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the null model for temperature — setup_temperature_null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_temperature_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the null model for temperature — setup_temperature_null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_eir.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up parameters and function for an eir-based travel_malaria model — setup_travel_eir","title":"Set up parameters and function for an eir-based travel_malaria model — setup_travel_eir","text":"Set parameters function eir-based travel_malaria model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_eir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up parameters and function for an eir-based travel_malaria model — setup_travel_eir","text":"","code":"setup_travel_eir(   pars,   travel_Opts = list(),   frac_time_spent_traveling = 0.01,   travel_eir_scale = 0,   travel_eir_t = NULL )"},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_eir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up parameters and function for an eir-based travel_malaria model — setup_travel_eir","text":"pars list travel_Opts list, overwrites default values frac_time_spent_traveling fraction time spent travel travel_eir_scale non-negative numeric value scale mean eir experienced traveling travel_eir_t temporal pattern eir experienced traveling","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_eir.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up parameters and function for an eir-based travel_malaria model — setup_travel_eir","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_foi.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up parameters and function for the FoI-based travel_malaria model — setup_travel_foi","title":"Set up parameters and function for the FoI-based travel_malaria model — setup_travel_foi","text":"Set parameters function FoI-based travel_malaria model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_foi.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up parameters and function for the FoI-based travel_malaria model — setup_travel_foi","text":"","code":"setup_travel_foi(pars, travel_Opts = list(), delta_scale = 0, delta_t = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_foi.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up parameters and function for the FoI-based travel_malaria model — setup_travel_foi","text":"pars list travel_Opts list, overwrites default values delta_scale non-negative numeric value scale mean travel_malaria FoI delta_t temporal pattern travel_malaria FoI","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_foi.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up parameters and function for the FoI-based travel_malaria model — setup_travel_foi","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_static.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to set up malaria importation — setup_travel_static","title":"A function to set up malaria importation — setup_travel_static","text":"Setup static model travel malaria","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to set up malaria importation — setup_travel_static","text":"","code":"setup_travel_static(pars, delta = 0)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to set up malaria importation — setup_travel_static","text":"pars list delta travel FoI","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to set up malaria importation — setup_travel_static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_vc_control.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for the control model of vector control (do nothing) — setup_vc_control","title":"Make parameters for the control model of vector control (do nothing) — setup_vc_control","text":"Make parameters control model vector control (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_vc_control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for the control model of vector control (do nothing) — setup_vc_control","text":"","code":"setup_vc_control(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_vc_control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for the control model of vector control (do nothing) — setup_vc_control","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_vc_control.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for the control model of vector control (do nothing) — setup_vc_control","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_vc_null.html","id":null,"dir":"Reference","previous_headings":"","what":"Distribute vector control, the null model — setup_vc_null","title":"Distribute vector control, the null model — setup_vc_null","text":"Distribute vector control, null model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_vc_null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Distribute vector control, the null model — setup_vc_null","text":"","code":"setup_vc_null(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_vc_null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Distribute vector control, the null model — setup_vc_null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_vc_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Distribute vector control, the null model — setup_vc_null","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_visitors_basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters and functions for the basic model for visitors — setup_visitors_basic","title":"Make parameters and functions for the basic model for visitors — setup_visitors_basic","text":"Make parameters functions basic model visitors","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_visitors_basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters and functions for the basic model for visitors — setup_visitors_basic","text":"","code":"setup_visitors_basic(   pars,   IMopts,   x_scale = 0,   xt = NULL,   V_scale = 0,   Vt = NULL )"},{"path":"https://dd-harp.github.io/exDE/reference/setup_visitors_basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters and functions for the basic model for visitors — setup_visitors_basic","text":"pars list IMopts list x_scale non-negative numeric value set mean x_visitors xt function change pattern x_visitors time V_scale non-negative numeric value set mean availability Visitors Vt function set temporal pattern availability Visitors","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_visitors_basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters and functions for the basic model for visitors — setup_visitors_basic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_visitors_static.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for the static model visitors (no visitors) — setup_visitors_static","title":"Make parameters for the static model visitors (no visitors) — setup_visitors_static","text":"Make parameters static model visitors (visitors)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_visitors_static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for the static model visitors (no visitors) — setup_visitors_static","text":"","code":"setup_visitors_static(pars, local_frac = 1, Visitors = 0, x_visitors = 0)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_visitors_static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for the static model visitors (no visitors) — setup_visitors_static","text":"pars list local_frac fraction humans / hosts visitors Visitors availability visitors x_visitors net infectiousness visitors","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_visitors_static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for the static model visitors (no visitors) — setup_visitors_static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_weather_forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the forced model for weather — setup_weather_forced","title":"Set up the forced model for weather — setup_weather_forced","text":"Set forced model weather","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_weather_forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the forced model for weather — setup_weather_forced","text":"","code":"setup_weather_forced(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_weather_forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the forced model for weather — setup_weather_forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_weather_forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the forced model for weather — setup_weather_forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_weather_null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the null model for weather — setup_weather_null","title":"Set up the null model for weather — setup_weather_null","text":"Set null model weather","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_weather_null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the null model for weather — setup_weather_null","text":"","code":"setup_weather_null(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_weather_null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the null model for weather — setup_weather_null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_weather_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the null model for weather — setup_weather_null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/shapeIt.html","id":null,"dir":"Reference","previous_headings":"","what":"Check the shape and dimensions of an object — shapeIt","title":"Check the shape and dimensions of an object — shapeIt","text":"Check shape dimensions object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/shapeIt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check the shape and dimensions of an object — shapeIt","text":"","code":"shapeIt(obj, d1, d2)"},{"path":"https://dd-harp.github.io/exDE/reference/shapeIt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check the shape and dimensions of an object — shapeIt","text":"obj numeric object d1 integer d2 integer","code":""},{"path":"https://dd-harp.github.io/exDE/reference/shapeIt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check the shape and dimensions of an object — shapeIt","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.eir.html","id":null,"dir":"Reference","previous_headings":"","what":"A model for travel malaria based on the eir in destinations — travel_malaria.eir","title":"A model for travel malaria based on the eir in destinations — travel_malaria.eir","text":"Implements travel_malaria model eir-based model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.eir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A model for travel malaria based on the eir in destinations — travel_malaria.eir","text":"","code":"# S3 method for eir travel_malaria(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.eir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A model for travel malaria based on the eir in destinations — travel_malaria.eir","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.eir.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A model for travel malaria based on the eir in destinations — travel_malaria.eir","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.foi.html","id":null,"dir":"Reference","previous_headings":"","what":"A model for the travel FoI — travel_malaria.foi","title":"A model for the travel FoI — travel_malaria.foi","text":"Implements travel_malaria model travel FoI","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.foi.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A model for the travel FoI — travel_malaria.foi","text":"","code":"# S3 method for foi travel_malaria(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.foi.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A model for the travel FoI — travel_malaria.foi","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.foi.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A model for the travel FoI — travel_malaria.foi","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulate travel malaria — travel_malaria","title":"Simulate travel malaria — travel_malaria","text":"method dispatches type pars$TRAVEL.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulate travel malaria — travel_malaria","text":"","code":"travel_malaria(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulate travel malaria — travel_malaria","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulate travel malaria — travel_malaria","text":"numeric value","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.static.html","id":null,"dir":"Reference","previous_headings":"","what":"travel, a static model — travel_malaria.static","title":"travel, a static model — travel_malaria.static","text":"Implements travel_malaria static model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"travel, a static model — travel_malaria.static","text":"","code":"# S3 method for static travel_malaria(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"travel, a static model — travel_malaria.static","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"travel, a static model — travel_malaria.static","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the initial values to the last values of the last simulation — update_inits","title":"Set the initial values to the last values of the last simulation — update_inits","text":"Set initial values last values last simulation","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the initial values to the last values of the last simulation — update_inits","text":"","code":"update_inits(y0, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the initial values to the last values of the last simulation — update_inits","text":"y0 vector initial values pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the initial values to the last values of the last simulation — update_inits","text":"y numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for the basic aquatic mosquito competition model — update_inits_L.basic","title":"Update inits for the basic aquatic mosquito competition model — update_inits_L.basic","text":"Update inits basic aquatic mosquito competition model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for the basic aquatic mosquito competition model — update_inits_L.basic","text":"","code":"# S3 method for basic update_inits_L(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for the basic aquatic mosquito competition model — update_inits_L.basic","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for the basic aquatic mosquito competition model — update_inits_L.basic","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the initial values from a vector of model states — update_inits_L","title":"Set the initial values from a vector of model states — update_inits_L","text":"method dispatches type pars$Lpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the initial values from a vector of model states — update_inits_L","text":"","code":"update_inits_L(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the initial values from a vector of model states — update_inits_L","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the initial values from a vector of model states — update_inits_L","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for the basic aquatic mosquito competition model — update_inits_L.trace","title":"Update inits for the basic aquatic mosquito competition model — update_inits_L.trace","text":"Update inits basic aquatic mosquito competition model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for the basic aquatic mosquito competition model — update_inits_L.trace","text":"","code":"# S3 method for trace update_inits_L(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for the basic aquatic mosquito competition model — update_inits_L.trace","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for the basic aquatic mosquito competition model — update_inits_L.trace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.GeRM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Update the initial values for GeRM adult mosquito model — update_inits_MYZ.GeRM_dde","title":"Update the initial values for GeRM adult mosquito model — update_inits_MYZ.GeRM_dde","text":"Update initial values GeRM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.GeRM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update the initial values for GeRM adult mosquito model — update_inits_MYZ.GeRM_dde","text":"","code":"# S3 method for GeRM_dde update_inits_MYZ(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.GeRM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update the initial values for GeRM adult mosquito model — update_inits_MYZ.GeRM_dde","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.GeRM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update the initial values for GeRM adult mosquito model — update_inits_MYZ.GeRM_dde","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.GeRM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for GeRM adult mosquito model — update_inits_MYZ.GeRM_ode","title":"Make inits for GeRM adult mosquito model — update_inits_MYZ.GeRM_ode","text":"Make inits GeRM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.GeRM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for GeRM adult mosquito model — update_inits_MYZ.GeRM_ode","text":"","code":"# S3 method for GeRM_ode update_inits_MYZ(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.GeRM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for GeRM adult mosquito model — update_inits_MYZ.GeRM_ode","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.GeRM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for GeRM adult mosquito model — update_inits_MYZ.GeRM_ode","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.Gtrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for Gtrace — update_inits_MYZ.Gtrace","title":"Update inits for Gtrace — update_inits_MYZ.Gtrace","text":"Update inits Gtrace","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.Gtrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for Gtrace — update_inits_MYZ.Gtrace","text":"","code":"# S3 method for Gtrace update_inits_MYZ(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.Gtrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for Gtrace — update_inits_MYZ.Gtrace","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for Gtrace — update_inits_MYZ.Gtrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.RM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for RM adult mosquito model — update_inits_MYZ.RM_dde","title":"Update inits for RM adult mosquito model — update_inits_MYZ.RM_dde","text":"Update inits RM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.RM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for RM adult mosquito model — update_inits_MYZ.RM_dde","text":"","code":"# S3 method for RM_dde update_inits_MYZ(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.RM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for RM adult mosquito model — update_inits_MYZ.RM_dde","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.RM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for RM adult mosquito model — update_inits_MYZ.RM_dde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.RM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for RM adult mosquito model — update_inits_MYZ.RM_ode","title":"Make inits for RM adult mosquito model — update_inits_MYZ.RM_ode","text":"Make inits RM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.RM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for RM adult mosquito model — update_inits_MYZ.RM_ode","text":"","code":"# S3 method for RM_ode update_inits_MYZ(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.RM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for RM adult mosquito model — update_inits_MYZ.RM_ode","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.RM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for RM adult mosquito model — update_inits_MYZ.RM_ode","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for Ztrace — update_inits_MYZ.Ztrace","title":"Update inits for Ztrace — update_inits_MYZ.Ztrace","text":"Update inits Ztrace","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for Ztrace — update_inits_MYZ.Ztrace","text":"","code":"# S3 method for Ztrace update_inits_MYZ(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for Ztrace — update_inits_MYZ.Ztrace","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for Ztrace — update_inits_MYZ.Ztrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for RM adult mosquito model — update_inits_MYZ.basicM","title":"Make inits for RM adult mosquito model — update_inits_MYZ.basicM","text":"Make inits RM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for RM adult mosquito model — update_inits_MYZ.basicM","text":"","code":"# S3 method for basicM update_inits_MYZ(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for RM adult mosquito model — update_inits_MYZ.basicM","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for RM adult mosquito model — update_inits_MYZ.basicM","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the initial values as a vector — update_inits_MYZ","title":"Set the initial values as a vector — update_inits_MYZ","text":"method dispatches type pars$MYZpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the initial values as a vector — update_inits_MYZ","text":"","code":"update_inits_MYZ(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the initial values as a vector — update_inits_MYZ","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the initial values as a vector — update_inits_MYZ","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for the SIP human model from a vector of states — update_inits_X.SIP","title":"Update inits for the SIP human model from a vector of states — update_inits_X.SIP","text":"Update inits SIP human model vector states","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for the SIP human model from a vector of states — update_inits_X.SIP","text":"","code":"# S3 method for SIP update_inits_X(pars, y0, i)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for the SIP human model from a vector of states — update_inits_X.SIP","text":"pars list y0 vector initial values host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for the SIP human model from a vector of states — update_inits_X.SIP","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for the SIS human model from a vector of states — update_inits_X.SIS","title":"Update inits for the SIS human model from a vector of states — update_inits_X.SIS","text":"Update inits SIS human model vector states","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for the SIS human model from a vector of states — update_inits_X.SIS","text":"","code":"# S3 method for SIS update_inits_X(pars, y0, i)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for the SIS human model from a vector of states — update_inits_X.SIS","text":"pars list y0 vector initial values host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for the SIS human model from a vector of states — update_inits_X.SIS","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for hybrid MoI human model from a vector of states — update_inits_X.hMoI","title":"Update inits for hybrid MoI human model from a vector of states — update_inits_X.hMoI","text":"Update inits hybrid MoI human model vector states","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for hybrid MoI human model from a vector of states — update_inits_X.hMoI","text":"","code":"# S3 method for hMoI update_inits_X(pars, y0, i)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for hybrid MoI human model from a vector of states — update_inits_X.hMoI","text":"pars list y0 vector initial values host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for hybrid MoI human model from a vector of states — update_inits_X.hMoI","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the initial values from a vector of states — update_inits_X","title":"Set the initial values from a vector of states — update_inits_X","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the initial values from a vector of states — update_inits_X","text":"","code":"update_inits_X(pars, y0, i)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the initial values from a vector of states — update_inits_X","text":"pars list y0 vector initial values host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the initial values from a vector of states — update_inits_X","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for the trace human model from a vector of states — update_inits_X.trace","title":"Update inits for the trace human model from a vector of states — update_inits_X.trace","text":"Update inits trace human model vector states","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for the trace human model from a vector of states — update_inits_X.trace","text":"","code":"# S3 method for trace update_inits_X(pars, y0, i)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for the trace human model from a vector of states — update_inits_X.trace","text":"pars list y0 vector initial values host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for the trace human model from a vector of states — update_inits_X.trace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn.html","id":null,"dir":"Reference","previous_headings":"","what":"Generalized spatial differential equation model — xDE_diffeqn","title":"Generalized spatial differential equation model — xDE_diffeqn","text":"Compute derivatives deSolve::ode deSolve::dede using generic methods model component.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generalized spatial differential equation model — xDE_diffeqn","text":"","code":"xDE_diffeqn(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generalized spatial differential equation model — xDE_diffeqn","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generalized spatial differential equation model — xDE_diffeqn","text":"list containing vector state derivatives","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_aquatic.html","id":null,"dir":"Reference","previous_headings":"","what":"Differential equation models for aquatic mosquito populations — xDE_diffeqn_aquatic","title":"Differential equation models for aquatic mosquito populations — xDE_diffeqn_aquatic","text":"Compute derivatives deSolve::ode deSolve::dede using generic methods model component.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_aquatic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Differential equation models for aquatic mosquito populations — xDE_diffeqn_aquatic","text":"","code":"xDE_diffeqn_aquatic(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_aquatic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Differential equation models for aquatic mosquito populations — xDE_diffeqn_aquatic","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_aquatic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Differential equation models for aquatic mosquito populations — xDE_diffeqn_aquatic","text":"list containing vector state derivatives","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_cohort.html","id":null,"dir":"Reference","previous_headings":"","what":"Differential equation models for human cohorts — xDE_diffeqn_cohort","title":"Differential equation models for human cohorts — xDE_diffeqn_cohort","text":"Compute derivatives deSolve::ode deSolve::dede using generic methods model component.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_cohort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Differential equation models for human cohorts — xDE_diffeqn_cohort","text":"","code":"xDE_diffeqn_cohort(a, y, pars, F_eir)"},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_cohort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Differential equation models for human cohorts — xDE_diffeqn_cohort","text":"age cohort y state vector pars list F_eir trace function returns eir","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_cohort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Differential equation models for human cohorts — xDE_diffeqn_cohort","text":"list containing vector state derivatives","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_human.html","id":null,"dir":"Reference","previous_headings":"","what":"Differential equations isolating the humans, forced with Ztrace — xDE_diffeqn_human","title":"Differential equations isolating the humans, forced with Ztrace — xDE_diffeqn_human","text":"Compute derivatives deSolve::ode deSolve::dede using generic methods model component.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_human.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Differential equations isolating the humans, forced with Ztrace — xDE_diffeqn_human","text":"","code":"xDE_diffeqn_human(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_human.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Differential equations isolating the humans, forced with Ztrace — xDE_diffeqn_human","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_human.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Differential equations isolating the humans, forced with Ztrace — xDE_diffeqn_human","text":"list containing vector state derivatives","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_mosy.html","id":null,"dir":"Reference","previous_headings":"","what":"Generalized spatial differential equation model (mosquito only) — xDE_diffeqn_mosy","title":"Generalized spatial differential equation model (mosquito only) — xDE_diffeqn_mosy","text":"Mirrors xDE_diffeqn includes adult aquatic mosquito components.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_mosy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generalized spatial differential equation model (mosquito only) — xDE_diffeqn_mosy","text":"","code":"xDE_diffeqn_mosy(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_mosy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generalized spatial differential equation model (mosquito only) — xDE_diffeqn_mosy","text":"t current simulation time y state vector pars list appropriate adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_mosy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generalized spatial differential equation model (mosquito only) — xDE_diffeqn_mosy","text":"list containing vector state derivatives","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_EIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the EIR vs. time — xde_lines_EIR","title":"Add lines for the EIR vs. time — xde_lines_EIR","text":"Add lines EIR vs. time","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_EIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the EIR vs. time — xde_lines_EIR","text":"","code":"xde_lines_EIR(terms, pars, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_EIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the EIR vs. time — xde_lines_EIR","text":"terms list outputs exDE::parse_deout() pars list defines exDE model (e.g.,  generated exDE::xde_setup()) clrs vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_M.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for adult mosquito population density — xde_lines_M","title":"Add lines for adult mosquito population density — xde_lines_M","text":"Add lines adult mosquito population density","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_M.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for adult mosquito population density — xde_lines_M","text":"","code":"xde_lines_M(MYZ, pars, clrs = \"darkblue\", llty = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_M.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for adult mosquito population density — xde_lines_M","text":"MYZ list output exDE::parse_deout() pars list defines exDE model (e.g.,  generated xde_setup()) clrs vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_PR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the prevalence / parasite rate (PR) from a model of human infection and immunity — xde_lines_PR","title":"Add lines for the prevalence / parasite rate (PR) from a model of human infection and immunity — xde_lines_PR","text":"Add lines prevalence / parasite rate (PR) model human infection immunity","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_PR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the prevalence / parasite rate (PR) from a model of human infection and immunity — xde_lines_PR","text":"","code":"xde_lines_PR(terms, pars, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_PR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the prevalence / parasite rate (PR) from a model of human infection and immunity — xde_lines_PR","text":"terms list outputs exDE::parse_deout() pars list defines exDE model (e.g.,  generated xde_setup()) clrs vector colors llty integer (integers) specifies lty plotting","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_X_SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the density of infected individuals for the SIP model — xde_lines_X_SIP","title":"Add lines for the density of infected individuals for the SIP model — xde_lines_X_SIP","text":"Add lines density infected individuals SIP model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_X_SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the density of infected individuals for the SIP model — xde_lines_X_SIP","text":"","code":"xde_lines_X_SIP(   XH,   pars,   clrs = c(\"darkblue\", \"darkred\", \"darkgreen\"),   llty = 1 )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_X_SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the density of infected individuals for the SIP model — xde_lines_X_SIP","text":"XH list outputs parse_deout_X_SIS pars list defines exDE model (e.g.,  generated xde_setup()) clrs vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_X_SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the density of infected individuals for the SIS model — xde_lines_X_SIS","title":"Add lines for the density of infected individuals for the SIS model — xde_lines_X_SIS","text":"Add lines density infected individuals SIS model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_X_SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the density of infected individuals for the SIS model — xde_lines_X_SIS","text":"","code":"xde_lines_X_SIS(XH, pars, clrs = c(\"darkblue\", \"darkred\"), llty = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_X_SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the density of infected individuals for the SIS model — xde_lines_X_SIS","text":"XH list outputs parse_deout_X_SIS pars list defines exDE model (e.g.,  generated xde_setup()) clrs vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_YZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the density of infected and infective mosquitoes — xde_lines_YZ","title":"Add lines for the density of infected and infective mosquitoes — xde_lines_YZ","text":"Add lines density infected infective mosquitoes","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_YZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the density of infected and infective mosquitoes — xde_lines_YZ","text":"","code":"xde_lines_YZ(MYZ, pars, Yclrs = \"purple\", Zclrs = \"darkred\", llty = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_YZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the density of infected and infective mosquitoes — xde_lines_YZ","text":"MYZ list output exDE::parse_deout() pars list defines exDE model (e.g.,  generated xde_setup()) Yclrs vector colors Zclrs vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_YZ_fracs.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the fraction of infected and infective mosquitoes — xde_lines_YZ_fracs","title":"Add lines for the fraction of infected and infective mosquitoes — xde_lines_YZ_fracs","text":"Add lines fraction infected infective mosquitoes","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_YZ_fracs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the fraction of infected and infective mosquitoes — xde_lines_YZ_fracs","text":"","code":"xde_lines_YZ_fracs(MYZ, pars, Yclrs = \"purple\", Zclrs = \"darkred\", llty = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_YZ_fracs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the fraction of infected and infective mosquitoes — xde_lines_YZ_fracs","text":"MYZ list output exDE::parse_deout() pars list defines exDE model (e.g.,  generated xde_setup()) Yclrs vector colors infected mosquitoes Zclrs vector colors infective mosquitoes llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_aEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the annualized EIR vs. time — xde_lines_aEIR","title":"Add lines for the annualized EIR vs. time — xde_lines_aEIR","text":"Add lines annualized EIR vs. time","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_aEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the annualized EIR vs. time — xde_lines_aEIR","text":"","code":"xde_lines_aEIR(terms, pars, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_aEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the annualized EIR vs. time — xde_lines_aEIR","text":"terms list outputs parse_deout() pars list defines exDE model (e.g.,  generated exDE::xde_setup()) clrs vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_EIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the EIR vs. time — xde_plot_EIR","title":"Plot the EIR vs. time — xde_plot_EIR","text":"Plot EIR vs. time","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_EIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the EIR vs. time — xde_plot_EIR","text":"","code":"xde_plot_EIR(pars, clrs = \"black\", llty = 1, stable = FALSE, add_axes = TRUE)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_EIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the EIR vs. time — xde_plot_EIR","text":"pars list defines exDE model (e.g.,  generated exDE::xde_setup()) clrs vector colors llty integer (integers) set lty plotting stable logical: set FALSE orbits TRUE stable_orbits add_axes logical: plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_M.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot adult mosquito population density — xde_plot_M","title":"Plot adult mosquito population density — xde_plot_M","text":"Plot adult mosquito population density","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_M.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot adult mosquito population density — xde_plot_M","text":"","code":"xde_plot_M(   pars,   s = 1,   clrs = \"darkblue\",   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_M.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot adult mosquito population density — xde_plot_M","text":"pars list defines exDE model (e.g.,  generated xde_setup()) s vector species index clrs vector colors llty integer (integers) set lty plotting stable logical: set FALSE orbits TRUE stable_orbits add_axes logical: plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_PR.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the prevalence / parasite rate (PR) from a model of human infection and immunity — xde_plot_PR","title":"Plot the prevalence / parasite rate (PR) from a model of human infection and immunity — xde_plot_PR","text":"Plot prevalence / parasite rate (PR) model human infection immunity","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_PR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the prevalence / parasite rate (PR) from a model of human infection and immunity — xde_plot_PR","text":"","code":"xde_plot_PR(pars, clrs = \"black\", llty = 1, stable = FALSE, add_axes = TRUE)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_PR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the prevalence / parasite rate (PR) from a model of human infection and immunity — xde_plot_PR","text":"pars list defines exDE model (e.g.,  generated xde_setup()) clrs vector colors llty integer (integers) specifies lty plotting stable logical: set FALSE orbits TRUE stable_orbits add_axes logical: plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the density of infected individuals for the SIP model — xde_plot_X.SIP","title":"Plot the density of infected individuals for the SIP model — xde_plot_X.SIP","text":"Plot density infected individuals SIP model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the density of infected individuals for the SIP model — xde_plot_X.SIP","text":"","code":"# S3 method for SIP xde_plot_X(   pars,   i = 1,   clrs = c(\"darkblue\", \"darkred\", \"darkgreen\"),   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the density of infected individuals for the SIP model — xde_plot_X.SIP","text":"pars list defines exDE model (e.g.,  generated xde_setup()) host species index clrs vector colors llty integer (integers) set lty plotting stable logical: set FALSE orbits TRUE stable_orbits add_axes logical: plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the density of infected individuals for the SIS model — xde_plot_X.SIS","title":"Plot the density of infected individuals for the SIS model — xde_plot_X.SIS","text":"Plot density infected individuals SIS model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the density of infected individuals for the SIS model — xde_plot_X.SIS","text":"","code":"# S3 method for SIS xde_plot_X(   pars,   i = 1,   clrs = c(\"darkblue\", \"darkred\"),   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the density of infected individuals for the SIS model — xde_plot_X.SIS","text":"pars list defines exDE model (e.g.,  generated xde_setup()) host species index clrs vector colors llty integer (integers) set lty plotting stable logical: set FALSE orbits TRUE stable_orbits add_axes logical: plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting for epidemiological models — xde_plot_X","title":"Basic plotting for epidemiological models — xde_plot_X","text":"Basic plotting epidemiological models","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting for epidemiological models — xde_plot_X","text":"","code":"xde_plot_X(   pars,   i = 1,   clrs = \"black\",   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting for epidemiological models — xde_plot_X","text":"pars list defines exDE model (e.g.,  generated xde_setup()) host species index clrs vector colors llty integer (integers) set lty plotting stable logical: set FALSE orbits TRUE stable_orbits add_axes logical: plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_YZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the density of infected and infective mosquitoes — xde_plot_YZ","title":"Plot the density of infected and infective mosquitoes — xde_plot_YZ","text":"Plot density infected infective mosquitoes","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_YZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the density of infected and infective mosquitoes — xde_plot_YZ","text":"","code":"xde_plot_YZ(   pars,   s = 1,   Yclrs = \"purple\",   Zclrs = \"darkred\",   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_YZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the density of infected and infective mosquitoes — xde_plot_YZ","text":"pars list defines exDE model (e.g.,  generated xde_setup()) s vector species index Yclrs vector colors infected mosquitoes Zclrs vector colors infective mosquitoes llty integer (integers) set lty plotting stable set FALSE orbits TRUE stable_orbits add_axes plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_YZ_fracs.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the fraction of infected and infective mosquitoes — xde_plot_YZ_fracs","title":"Plot the fraction of infected and infective mosquitoes — xde_plot_YZ_fracs","text":"Plot fraction infected infective mosquitoes","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_YZ_fracs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the fraction of infected and infective mosquitoes — xde_plot_YZ_fracs","text":"","code":"xde_plot_YZ_fracs(   pars,   s = 1,   Yclrs = \"purple\",   Zclrs = \"darkred\",   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_YZ_fracs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the fraction of infected and infective mosquitoes — xde_plot_YZ_fracs","text":"pars list defines exDE model (e.g.,  generated xde_setup()) s vector species index Yclrs vector colors infected mosquitoes Zclrs vector colors infective mosquitoes llty integer (integers) set lty plotting stable logical, set FALSE orbits TRUE stable_orbits add_axes logical plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_aEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the annualized EIR vs. time — xde_plot_aEIR","title":"Plot the annualized EIR vs. time — xde_plot_aEIR","text":"Plot annualized EIR vs. time","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_aEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the annualized EIR vs. time — xde_plot_aEIR","text":"","code":"xde_plot_aEIR(pars, clrs = \"black\", llty = 1, stable = FALSE, add_axes = TRUE)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_aEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the annualized EIR vs. time — xde_plot_aEIR","text":"pars list defines exDE model (e.g.,  generated exDE::xde_setup()) clrs vector colors llty integer (integers) set lty plotting stable logical: set FALSE orbits TRUE stable_orbits add_axes logical: plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up a model for xde_diffeqn — xde_setup","title":"Set up a model for xde_diffeqn — xde_setup","text":"Set model xde_diffeqn","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up a model for xde_diffeqn — xde_setup","text":"","code":"xde_setup(   modelName = \"unnamed\",   MYZname = \"RM\",   Xname = \"SIS\",   Lname = \"trace\",   nPatches = 1,   nVectors = 1,   nHosts = 1,   HPop = 1000,   membership = 1,   MYZopts = list(),   calK = \"herethere\",   calKopts = list(),   EIPname = \"static\",   EIPopts = list(),   Xopts = list(),   BFopts = list(),   residence = 1,   searchB = 1,   F_circadian = NULL,   TimeSpent = \"athome\",   TimeSpentOpts = list(),   searchQ = 1,   Lopts = list() )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up a model for xde_diffeqn — xde_setup","text":"modelName name model (arbitrary) MYZname character string defining MYZ model Xname character string defining X model Lname character string defining L model nPatches number patches nVectors number vector species nHosts number vertebrate host species HPop number humans patch membership vector describes patch aquatic habitat found MYZopts list configure MYZ model calK either calK matrix string defines set calKopts options setup calK EIPname options setup EIPmod EIPopts options setup EIPmod Xopts list configure X model BFopts list configure blood feeding model residence vector describes patch human stratum lives searchB vector search weights blood feeding F_circadian function describing mosquito daily activity TimeSpent either TimeSpent matrix string call function sets TimeSpentOpts options setup TimeSpent searchQ vector search weights egg laying Lopts list configure L model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up a model for xde_diffeqn — xde_setup","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_aquatic.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up a model for xde_diffeqn_aqua — xde_setup_aquatic","title":"Set up a model for xde_diffeqn_aqua — xde_setup_aquatic","text":"Set model xde_diffeqn_aqua","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_aquatic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up a model for xde_diffeqn_aqua — xde_setup_aquatic","text":"","code":"xde_setup_aquatic(   modelName = \"unnamed\",   nHabitats = 1,   nVectors = 1,   Lname = \"basic\",   Lopts = list(),   MYZopts = list(),   LSMname = \"null\" )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_aquatic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up a model for xde_diffeqn_aqua — xde_setup_aquatic","text":"modelName name model (arbitrary) nHabitats number habitats nVectors number vector species Lname character string defining L model Lopts list configure L model MYZopts list configure F_eggs Gtrace model LSMname character string defining LSM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_aquatic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up a model for xde_diffeqn_aqua — xde_setup_aquatic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_cohort.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up a model for xde_diffeqn_cohort — xde_setup_cohort","title":"Set up a model for xde_diffeqn_cohort — xde_setup_cohort","text":"Set model xde_diffeqn_cohort","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_cohort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up a model for xde_diffeqn_cohort — xde_setup_cohort","text":"","code":"xde_setup_cohort(   F_eir,   modelName = \"unnamed\",   Xname = \"SIS\",   HPop = 1000,   searchB = 1,   residence = 1,   Xopts = list() )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_cohort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up a model for xde_diffeqn_cohort — xde_setup_cohort","text":"F_eir function F_eir(t, pars) returns daily FoI modelName name model (arbitrary) Xname character string defining X model HPop number humans patch searchB vector search weights blood feeding residence vector describes patch human stratum lives Xopts list configure X model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_cohort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up a model for xde_diffeqn_cohort — xde_setup_cohort","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_human.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up a model for xde_diffeqn_human — xde_setup_human","title":"Set up a model for xde_diffeqn_human — xde_setup_human","text":"Set model xde_diffeqn_human","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_human.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up a model for xde_diffeqn_human — xde_setup_human","text":"","code":"xde_setup_human(   modelName = \"unnamed\",   Xname = \"SIS\",   HPop = 1000,   MYZopts = list(),   Xopts = list(),   BFopts = list(),   residence = 1,   searchB = 1,   F_circadian = NULL,   TimeSpent = \"athome\",   TimeSpentOpts = list() )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_human.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up a model for xde_diffeqn_human — xde_setup_human","text":"modelName name model (arbitrary) Xname character string defining X model HPop number humans patch MYZopts list configure MYZ model Xopts list configure X model BFopts list configure blood feeding model residence vector describes patch human stratum lives searchB vector search weights blood feeding F_circadian function describing mosquito daily activity TimeSpent either TimeSpent matrix string call function sets TimeSpentOpts options setup TimeSpent","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_human.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up a model for xde_diffeqn_human — xde_setup_human","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_mosy.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up a model for xde_diffeqn_mosy — xde_setup_mosy","title":"Set up a model for xde_diffeqn_mosy — xde_setup_mosy","text":"Set model xde_diffeqn_mosy","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_mosy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up a model for xde_diffeqn_mosy — xde_setup_mosy","text":"","code":"xde_setup_mosy(   modelName = \"unnamed\",   MYZname = \"basicM\",   Lname = \"basic\",   nPatches = 1,   nVectors = 1,   membership = 1,   MYZopts = list(),   calK = \"herethere\",   calKopts = list(),   searchQ = 1,   Lopts = list(),   kappa = NULL )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_mosy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up a model for xde_diffeqn_mosy — xde_setup_mosy","text":"modelName name model (arbitrary) MYZname character string defining MYZ model Lname character string defining L model nPatches number patches nVectors number vector species membership vector describes patch aquatic habitat found MYZopts list configure MYZ model calK either calK matrix string defines set calKopts options setup calK searchQ vector search weights egg laying Lopts list configure L model kappa values -- net infectivity force adult infection dynamics","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_mosy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up a model for xde_diffeqn_mosy — xde_setup_mosy","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.aqua.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua","title":"Solve a system of equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua","text":"Implements xde_solve aquatic dynaamic","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.aqua.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua","text":"","code":"# S3 method for aqua xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.aqua.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.aqua.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.aqua_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of delay equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua_dde","title":"Solve a system of delay equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua_dde","text":"Implements xde_solve aquatic dynaamic","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.aqua_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of delay equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua_dde","text":"","code":"# S3 method for aqua_dde xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.aqua_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of delay equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua_dde","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.aqua_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of delay equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua_dde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.cohort.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of equations with xDE_diffeqn_cohort — xde_solve.cohort","title":"Solve a system of equations with xDE_diffeqn_cohort — xde_solve.cohort","text":"Implements xde_solve mosquito dynamics (transmission)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.cohort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of equations with xDE_diffeqn_cohort — xde_solve.cohort","text":"","code":"# S3 method for cohort xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.cohort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of equations with xDE_diffeqn_cohort — xde_solve.cohort","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.cohort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of equations with xDE_diffeqn_cohort — xde_solve.cohort","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of equations as a dde — xde_solve.dde","title":"Solve a system of equations as a dde — xde_solve.dde","text":"Implements xde_solve delay differential equations","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of equations as a dde — xde_solve.dde","text":"","code":"# S3 method for dde xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of equations as a dde — xde_solve.dde","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of equations as a dde — xde_solve.dde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of equations — xde_solve","title":"Solve a system of equations — xde_solve","text":"method dispatches type pars$xde.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of equations — xde_solve","text":"","code":"xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of equations — xde_solve","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of equations — xde_solve","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.human.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of equations with xDE_diffeqn_human — xde_solve.human","title":"Solve a system of equations with xDE_diffeqn_human — xde_solve.human","text":"Implements xde_solve mosquito dynamics (transmission)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.human.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of equations with xDE_diffeqn_human — xde_solve.human","text":"","code":"# S3 method for human xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.human.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of equations with xDE_diffeqn_human — xde_solve.human","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.human.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of equations with xDE_diffeqn_human — xde_solve.human","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.mosy.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy","title":"Solve a system of equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy","text":"Implements xde_solve mosquito dynamics (transmission)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.mosy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy","text":"","code":"# S3 method for mosy xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.mosy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.mosy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.mosy_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of delay differential equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy_dde","title":"Solve a system of delay differential equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy_dde","text":"Implements xde_solve mosquito dynamics (transmission)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.mosy_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of delay differential equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy_dde","text":"","code":"# S3 method for mosy_dde xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.mosy_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of delay differential equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy_dde","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.mosy_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of delay differential equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy_dde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of equations as an ode — xde_solve.ode","title":"Solve a system of equations as an ode — xde_solve.ode","text":"Implements xde_solve ordinary differential equations","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of equations as an ode — xde_solve.ode","text":"","code":"# S3 method for ode xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of equations as an ode — xde_solve.ode","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of equations as an ode — xde_solve.ode","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_stable_orbit.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve for the steady state or stable orbit of a system of equations — xde_stable_orbit","title":"Solve for the steady state or stable orbit of a system of equations — xde_stable_orbit","text":"method dispatches type pars$xde.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_stable_orbit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve for the steady state or stable orbit of a system of equations — xde_stable_orbit","text":"","code":"xde_stable_orbit(pars, Ymax = 10)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_stable_orbit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve for the steady state or stable orbit of a system of equations — xde_stable_orbit","text":"pars list defines model Ymax number years burn-","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_stable_orbit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve for the steady state or stable orbit of a system of equations — xde_stable_orbit","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_steady.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve for the steady state of a system of equations using rootSolve::steady — xde_steady","title":"Solve for the steady state of a system of equations using rootSolve::steady — xde_steady","text":"method dispatches type pars$xde","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_steady.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve for the steady state of a system of equations using rootSolve::steady — xde_steady","text":"","code":"xde_steady(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_steady.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve for the steady state of a system of equations using rootSolve::steady — xde_steady","text":"pars list defines model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_steady.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve for the steady state of a system of equations using rootSolve::steady — xde_steady","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/news/index.html","id":"exde-100","dir":"Changelog","previous_headings":"","what":"exDE 1.0.0","title":"exDE 1.0.0","text":"CRAN release: 2022-11-18 Extensive update include exogenous forcing weather, climate, etc. well vector control, including ITN-based model vector control Extended documentation Extended testing Include CITATION file pre-print Re-submit CRAN","code":""},{"path":"https://dd-harp.github.io/exDE/news/index.html","id":"exde-010","dir":"Changelog","previous_headings":"","what":"exDE 0.1.0","title":"exDE 0.1.0","text":"Initial release exDE CRAN.","code":""}]
+[{"path":"https://dd-harp.github.io/exDE/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2022 exDE authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"sec1","dir":"Articles","previous_headings":"","what":"Git workflow","title":"Contributing","text":"exDE project hosted GitHub (repository), use Git workflow similar “Gitflow” (albeit without separate release branch, main takes role), described . Git workflow way use repository way invite collaboration organized way protects latest stable version software unintended changes. new Git need reminders, please check excellent documentation Atlassian. recommend reading “Getting Started” learn set repository, followed “Collaborating” learn work branches, pull requests, merging, common Git activities. workflow designed around branches. main, dev, gh-pages branches always exist repository. branches exist long person(s) working need , deleted merged dev. main: branch contains latest version release exDE, updated CRAN version also updated. PRs submitted except core dev team, updated main mean need update package CRAN various housekeeping tasks accompany version update (.e. create archival release update accepted CRAN). dev: branch PRs collaborators made . version code dev always useable (.e. pass automated tests), contain latest cutting edge features. Periodically dev accumulated sufficient number new features, member core dev team make PR dev main. main updated update CRAN package, often, CRAN request package maintainers submit updates “every 1–2 months”. gh-pages: branch exists support GitHub pages website (one browsing right now). updated automatically pkgdown continuous integration workflow rebuilds website main pushed (.e. PR merged main). gh-pages considered “read-” branch, even core dev team. feat/*: branches starting feat/ collaborators (core dev) names branches updating including new features, including limited code, documentation, tests. example, branch improved documentation document called feat/UpdateContributing. PR feat/ branch merged dev, feat/ branch deleted. PRs never made feat/ branches main. bugfix/*: small bugfixes (spelling errors, misnamed variables, etc), may appropriate make bugfix/ branch. rules apply feat/ branches. branches use GitHub’s branch protection rules enforce rules. Core dev team members can access going Settings -> Branches. main dev protected deletion. PRs made dev must reviewed approved least 1 reviewer allowed merged.  show example workflow . main branch, blue, starts left side, dev created , purple. , two feat/* bugfix/* branches created dev time, shown green. upper one two updates merged back dev, via pull request. pull request, lower one must pull updates dev working latest version code. another update, ready merged dev via pull request. point, decide two features enough version update, make pull request dev main update version 0.1. merged, can start making feat/* bugfix/* branches dev start developing version 0.2!","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"example","dir":"Articles","previous_headings":"Git workflow","what":"Example","title":"Contributing","text":"Let’s say great idea new feature, change improve document. ’s get started Git workflow get feature road merged exDE software. Please note, assume familiarity Git commands . reference meaning commands, please see Git documentation. start work exDE, first clone repository. terminal window, navigate directory want exDE folder appear , run git clone git@github.com:dd-harp/exDE.git, use SSH keys, git clone https://github.com/dd-harp/exDE.git clone HTTPS. links can found click green “Code” button main repository page. clone repository, go inside cd exDE. run git fetch --retrieves information branches remote (repository GitHub website) local repository (one computer). Now switch dev branch git checkout dev. can make sure ’s date running git pull origin dev. Let’s say want call new feature branch feat/UpdateContributing. can make switch running git checkout -b feat/UpdateContributing. push new branch remote repository, run git push origin feat/UpdateContributing. now appear list branches. Now, make changes! recommend editing package RStudio using R project file exDE.Rproj repository. explained Section 3. ready push changes, use git add either add files commit one one, know want add new /modified files, can use git add .. Run git commit -m \"message explaining changes \" make commit message. mind many small commits, Git style, please feel pressure make large commits. Now git push origin feat/UpdateContributing push commit remote branch feat/UpdateContributing! navigate branch GitHub repository, see changes. Now repeat steps 6 9 ready start testing changes submit pull request (covered Sections 4 5).","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"sec2","dir":"Articles","previous_headings":"","what":"The exDE R package","title":"Contributing","text":"exDE R package, going making substantial changes, necessary sense organized package must rebuilt creating documentation, exporting functions, testing. extensive documentation R package structured comes official R manual, Writing R Extensions. shorter guide tips current best practice book R Packages, unfamiliar R packages, reccomend briefly skimming book starting point. building exDE supported pkgdown, responsible automatically building documentation website browsing right now, testthat used test package. files top level directory important aware : _pkgdown.yml: controls website generated, explained article. add delete functions objects documentation package, add delete vignettes, must modify file website build properly. DESCRIPTION: file provides critical information package, documentation official manual R packages book. updated version releases, include additional authors, add additional packages Imports Suggests. NAMESPACE: read-file produced running roxygen2 build documentation package, tells R functions exported package user’s R session load exDE library(exDE). never modified hand. NEWS.md: NEWS page package’s CRAN page well News tab GitHub pages website built file; modified dev team ready update main new version. information, see utils::news help file. README.md: main readme file displayed GitHub repository, main page GitHub pages website, README page package’s CRAN page. rest package organized directories. detail, recommend reading guides linked earlier. .github/: files control GitHub Actions used automatically test package PR made, automatically build package website, automatically check code coverage (% code checked tests). Much detail given Section 6. docs/: contains pkgdown website built pushed gh-pages automatically GitHub Action. trigger manual (local) build website test something using pkgdown::build_site, build folder. folder considered read-. inst/: folder serves many purposes general R packages (see resources details), currently contains CITATION file used generate citation found utils::citation. man/: folder contains package function/object documentation automatically generated roxygen2, considered read-. R/: source code package lives ; describe naming convention files can quickly identify existing code , organize name new code. tests/: within folder sub-directory testthat/ contains automated tests included package. test models initialized equilibrium remain equilibrium integrated time. vignettes/: folder contains .Rmd files contains vignettes R package, longer form articles document specific functionality exDE. available GitHub pages website via top drop menus package’s CRAN page.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"r-folder","dir":"Articles","previous_headings":"The exDE R package","what":"R/ folder","title":"Contributing","text":"model component “base” file ending -interface defines generic interface model component must implement. example human-interface.R defines generic methods human disease model must implement human-SIS.R defines specific methods SIS model human disease dynamics. adult-GeRM.R: generalized Ross-Macdonald model adult mosquito dynamics. aquatic-basic.R: basic competition model aquatic mosquito dynamics. aquatic-trace.R: trace (exogenously forced) model aquatic mosquito dynamics. human-SIS.R: SIS model human disease dynamics. human-SIP.R: SIP model human disease dynamics. human-hMoI.R: hybrid MoI model human disease dynamics. exogenous-null: null () exogenous forcing. vc-null.R: null () vector control. vc-lemenach.R: Le Menach model ITN based adult vector control. diffeqn.R: exDE generalized differential equations implement framework; typically modified. metrics.R: spatial metrics (defined Spatial Dynamics paper) utils.R: utility functions","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"sec3","dir":"Articles","previous_headings":"","what":"Making large changes or additions to exDE","title":"Contributing","text":"reading Section 2 reasonable grasp exDE R package organized, really understand implement new models, detail necessary files one actually modify add. also describe best practices contributors add package making large change. Let’s say someone wanted add new human disease model, say SIR model. basic steps : Within R/, make new file human-SIR.R implement generic methods human-interface.R new model. Also make function named something like make_parameters_human_SIR modify parameter environment implement SIR model. can check human disease models reference. RStudio, run Build -> Document (control/command + shift + D) run roxygen2 builds functions documentation updates NAMESPACE new functions. run Build -> Install Package (control/command + shift + B) re-install load package. works opened exDE.Rproj file RStudio project. Make new vignette named something like “human_vignette.Rmd” vignettes/ describing model parameters, perhaps simple simulation . Make test named something like test-human-sir.R tests/testthat/ tests SIR model behaves expected conditions outcome known (e.g. infected persons present, number susceptible persons can never decrease). Please see testthat documentation R packages chapter testing information. added new functions vignettes, add _pkgdown.yml file appropriate place. can use pkgdown::build_site point test website still builds. go details test package locally Section 4 make pull request Section 5. writing new model modifying existing one, please note exDE achieves modularity extensive use S3 dispatch, similar single dispatch programming languages. details base::UseMethod S3 chapter Advanced R. Use S3 dispatch appears extensively source code exDE. writing new functions, must documented. , existing code provides good reference. exDE depends upon roxygen2 build documentation, website provides help write appropriate tags (e.g. #' @export makes function appear exDE NAMESPACE).","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"sec4","dir":"Articles","previous_headings":"","what":"How to test locally","title":"Contributing","text":"making changes exDE submitting PR, take time local tests make sure package still works. extremely important make sure implement changes, re-document re-install package. RStudio, Build -> Document (control/command + shift + D) re-documents package Build -> Install Package (control/command + shift + B) re-installs package. Without package NAMESPACE file may include changes, library(exDE) using recent version code.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"testthat","dir":"Articles","previous_headings":"How to test locally","what":"testthat","title":"Contributing","text":"added tests, changed existing code want make sure tests still pass, run testthat::test_local run tests. error warning appears, re-run tests make sure false positive (due numerical precision errors, small fraction tests give false positive results). error comes consistently, please fix offending code continuing onward. Remember, tests run tests/testthat can check code specifically put tested! large changes tests cover functionality cases expected behavior known advance. unsure make appropriate tests, please either consult existing test files, make PR without tests tell reviewer yet included tests need help making .","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"devtools","dir":"Articles","previous_headings":"How to test locally","what":"devtools","title":"Contributing","text":"crucial function use devtools::check; includes running local tests also extensive set additional checks R CMD check (see official documentation exactly ). also rebuilds vignettes, takes longer just running tests, normally done seldom, one ready submit PR.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"pkgdown","dir":"Articles","previous_headings":"How to test locally","what":"pkgdown","title":"Contributing","text":"always good idea make sure package website still builds making changes. added removed functions, changed function names, added removed vignettes, need updated _pkgdown.yml accordingly. make sure everything works expected, run pkgdown::build_site, build website locally docs/ folder (open automatically browser done). Please address problems builds successfully.","code":""},{"path":[]},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"how-to-make-a-pr","dir":"Articles","previous_headings":"How to make or review a pull request","what":"How to make a PR","title":"Contributing","text":"point, might little tired reading, maybe somewhat anxious actually contributing . good time say making PR can absolutely collaborative process. following previous sections local tests working, think idea new feature work good addition exDE, please consider submitting PR tagging persons dev team can help get past finish line. make pull request, first, navigate branch made changes (.e. feat/* bugfix/* branch). open PR, follow GitHub documentation Atlassian documentation, remember PRs made dev (e.g. dev “base”). making PR, prompted enter description explains PR . Please ensure PR include many disparate modifications, represents self-contained piece work (.e. submit PRs change human mosquito model; please submit two separate PRs ). Please make sure text description contains following elements: PR addresses solves active issue, tag PR (.e. addresses issue 75, type text box #75 GitHub automatically link two; can also just type # GitHub begin automatically link open issues). PR adds new files R/, tests/testthat, vignettes please list write brief description one. apply auto-generated files (.e. anything docs/, man/, NAMESPACE). PR significantly modifies files, please list write brief descriptions changed. apply auto-generated files (.e. anything docs/, man/, NAMESPACE). -progress PR (.e. tests pass), please tag someone team help describe specific problems encountering. Finally, crucial, select someone review PR using “Reviewers” tab upper right hand corner page. PR merged dev passed review least one team member. point review process can start. reviewer may ask additional changes, remember keep making branch working . PR merged dev, please delete old feat/* bugfix/* branch.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"how-to-review-a-pr","dir":"Articles","previous_headings":"How to make or review a pull request","what":"How to review a PR","title":"Contributing","text":"requested reviewer, ’s responsibility : Evaluate whether proposed addition within scope software (e.g. directly-transmitted diseases outside scope exDE). Ensure PR made dev . code passing tests, identify problems suggest solutions author (see Section 6 details ). PR makes significant modifications exDE, work author (already done ) PR tests vignettes document new functions, added _pkgdown.yml file new features appear website. general, exDE’s design philosophy elegant clear design mirrors mathematical description model preferred fast code cases decision made, please correct obvious inefficiencies (e.g. aware matrix operations try structure parentheses minimize computational cost). confident can provide helpful review addresses (possibly) mathematical, conceptual, design, software issues related PR, please either pass someone else bring additional reviewers. Please either familiar review GitHub docs review PRs. cases may necessary investigate issues locally, branch merged. Assuming branch called feat/MyFeature, : Navigate exDE repository computer git fetch --update information branches present remote git checkout -b feat/MyFeature switch branch git pull origin feat/MyFeature make sure includes recent commits Investigate locally, may push fixes feat/MyFeature sure alert PR author done may expect reviewer make changes branch problems resolved CI tests pass, PR ready merged dev! may want delete merged branch let author know can point.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"sec6","dir":"Articles","previous_headings":"","what":"How to deal with continuous integration","title":"Contributing","text":"exDE use GitHub Actions automatically run continuous integration workflows, automated scripts run triggered certain events (.e. PRs pushing certain branches). 3 workflows run can found .github/workflows: check-standard.yaml: runs R CMD check several common operating systems (see official documentation ). runs time pull request made main dev. pkgdown.yaml: runs pkgdown::build_site_github_pages pushes new website gh-pages branch. runs pushes main (.e. PR merged main) new GitHub release made. test-coverage.yaml: runs covr::codecov updates exDE’s codecov integration. runs pushes main. three workflows standard R packages, originated https://github.com/r-lib/actions. workflows may encounter errors. panic happens. Errors can investigated clicking failing workflow Actions tab, clicking specific failing job(s) left hand side screen “Jobs”. errors displayed. Github Actions documentation also describes diagnose errors. Errors R-CMD-check stemming tests may sometimes due numerical errors; exDE can solve model floating point errors, sometimes false positive errors reported numerical routines encounter problems. Restart tests clicking “Re-run jobs” upper right hand see errors persist. Errors pkgdown likely cause ill-formed _pkgdown.yml file, please consult pkgdown documentation post issue get help. Finally encounter truly strange errors workflows (e.g. software installed, strange operating system specific errors, etc), may .yaml workflow scripts outdated need updated. case find latest updated workflow scripts https://github.com/r-lib/actions/tree/v2-branch/examples. , careful overwrite existing rules execute workflows (.e. update line name onward). can push update branch bugfix/check-standard.yaml, update workflow, example.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"sec7","dir":"Articles","previous_headings":"","what":"How to get ready for a version update","title":"Contributing","text":"(dev team ) sufficient number new features added dev version number exDE increased, sufficient duration time passed since last update CRAN (“every 1–2 months”), time make PR dev main get ready update software. please make sure: open PRs (please resolve close updating version) feat/* bugfix/* branches deleted resolving open PRs update NEWS.md new version number significant additions (consider making links NEWS.md PRs included update) update DESCRIPTION new version number make sure website still builds (test devtools::build_site) please use rhub builder service check package builds without errors Windows using CRAN standards (can use function rhub::check_for_cran ) now ready create PR dev main. following standard procedure (Section 5) exception deleting dev (protected deletion), ready update CRAN version exDE. : make update file cran-comments.md informing CRAN version update, tests pass, etc; follow guide R packages book. use devtools::release actually submit package CRAN, function asks many useful questions make sure package actually ready submitted. new version accepted CRAN make new GitHub release accompany new version. celebrate, go rest.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Contributing.html","id":"sec8","dir":"Articles","previous_headings":"","what":"How to report bugs or raise issues?","title":"Contributing","text":"expect common way users interact GitHub issues tab. first point contact exDE team, please hesitate raise issues may either bug reports, questions, comments/suggestions. prefer rather less communication. considering large feature changes, may nice discuss dev team issue first making feat/* branch submitting PR; also great time solicit collaboration feature development! find bug, please remember include minimum reproducible example bug R code addition describing wrong. Please remember include: exDE version Operating System R version Steps recreate Expected behavior Actual behavior Minimum reproducible example (R code)","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Understanding exDE","text":"goal developing exDE lower costs developing models (e.g. time spent formulating, coding, verifying, debugging, & etc.) realistic enough support decisions affecting malaria policies. operating assumption developing framework software robust decision support malaria policies put demands model-building differ expected scientific publication. models work policy setting, must realistic enough relevant policy discussions. ways, need realism associated computational complexity drove development several comprehensive individual-based models (IBMs), OpenMalaria, eMod, MalariaTools. models developed systems differential equations can replicate advantages come individual-based, wanted software handle computational complexity just well IBMs. advantage using systems differential equations resulting models much easier analyze. wanted framework scale complexity, start simple model, progressively modifying models add realism including: realistic human demography, including age structure, births & deaths, migration. multiple host vector species types spatial heterogeneity spatial dynamics, including human mobility mosquito dispersal realistic mosquito ecology exogenous forcing weather factors time, wanted flexibility isolate analyze various components model. Since framework modular, possible pass inputs one () dynamical components trace function, rather fully coupled model. trivial models also provide way rigorously pressure testing software. think model defining skill set, output variables naturally represent subset possible features, framework make easy build models right subset features. models – Einstein suggested – simple possible, simpler. people agree Einstein principle, provided usable advice . know model right level complexity? One way develop least one model clearly complex provide rigorous model selection suite models varying levels complexity. support decisions affecting malaria policy, model building must nimble. malaria programs integrate sophisticated analytics decision-making, conversation room can shift. time, programmatic priorities needs can change. keep , model builders capability building new models address new concerns. might possible real time, possible new model developed preliminary results within week . goals mind, developed mathematical framework make computation dynamical systems modular. mathematical basis modularity described Spatial Dynamics Malaria Transmission. also developed vignette describes modular forms use describe models implemented exDE.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"structural-elements","dir":"Articles","previous_headings":"","what":"Structural Elements","title":"Understanding exDE","text":"model several parameters describe structure model: nVectors – number distinct mosquito vector species model nHosts – number distinct vertebrate host species model HPop – population density population strata vertebrate host species. length HPop used set value nStrata nPatches – number distinct patches model. nHabitats – number distinct aquatic habitats model. Additional information needed configure model egg laying (see ): membership vector required: \\(^{th}\\) element membership matrix identifies patch belongs. searchQ vector required: \\(^{th}\\) element gives habitat search weight compute egg laying. MYZname – string, corresponding model exDE library, specifies model family adult mosquitoes Lname – string, corresponding model exDE library, specifies model family aquatic mosquito population dynamics used Xname – string, corresponding model exDE library, specifies model family human infection dynamics used","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"dynamical-components","dir":"Articles","previous_headings":"","what":"Dynamical Components","title":"Understanding exDE","text":"developing mathematical framework, identified three inseparable chunks model need internally coherent represented several different ways. chunks represented five distinct processes: Models human ecology parasite / pathogen infection dynamics appear one dynamical component. part computes dynamics infection immunity called \\(\\cal X\\), part describes human demography called \\(\\cal H.\\) two components can’t separated easy way, call chunk \\(\\cal XH\\). derivatives model class \\(\\cal X\\) type computed S3 function dXdt(t, y, pars) parameters model object called Xpar dXdt dispatches class(Xpar) Since multiple host species, Xpar \\(^{th}\\) species pars$Xpar[[]]. demographic model, \\(\\cal H\\), can configured part \\(\\cal X\\) Models adult mosquito ecology parasite / pathogen infection dynamics appear second dynamical component. part computes dynamics infection called \\(\\cal YZ\\), part computes mosquito population dynamics called \\(\\cal M\\). two components can’t separated easy way, call chunk \\(\\cal MYZ\\). derivatives model type computed S3 function dMYZdt(t, y, pars) dMdt(t, y, pars) parameters model object called MYZpar dMYZdt dispatches class(MYZpar) Since multiple host species, MYZpar \\(^{th}\\) species pars$MYZpar[[]]. Models aquatic mosquito ecology called \\(\\cal L\\). derivatives model type computed S3 function dLdt(t, y, pars) dMdt(t, y, pars) parameters model object called Lpar dLdt dispatches class(Lpar) Since multiple host species, Lpar \\(^{th}\\) species pars$Lpar[[]].","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"interfaces","dir":"Articles","previous_headings":"","what":"Interfaces","title":"Understanding exDE","text":"developing modular framework, recognized need develop rigorous yet flexible interface allow different dynamical components interact. connect two dynamical components, developed two well-defined interfaces: blood feeding egg laying.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"blood-feeding","dir":"Articles","previous_headings":"Interfaces","what":"Blood Feeding","title":"Understanding exDE","text":"model blood feeding parasite / pathogen transmission mosquitoes. model constrain mosquito blood feeding rates human fraction sensible ways. possible set values mosquito bionomic parameters static values constrained. Spatial Dynamics Malaria Transmission, introduce fully defined blood feeding module constrains blood feeding rate human fraction using concept resource availability. nPatches\\(>1\\) nStrata\\(>1\\), necessary supply additional information configure mixing matrix, \\(\\beta\\), attached pars$beta[[]][[s]] \\(^{th}\\) host \\(s^{th}\\) vector species. time spent matrix must configured host species vector blood feeding search weights must provided stratum, species. \\(^{th}\\) element \\(s^{th}\\) vector used compute availability hosts blood feeding. circadian weighting function required vector species, used transform \\(^{th}\\) time spent matrix set nVectors matrices describing time risk. demographic matrix must configured mosquito species describes mosquito survival dispersal patches.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"egg-laying","dir":"Articles","previous_headings":"Interfaces","what":"Egg Laying","title":"Understanding exDE","text":"description locations aquatic habitats model egg laying emergence. membership vector must provided: \\(^{th}\\) element index patch habitat found search vector must provided: \\(^{th}\\) element index patch habitat found","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"human-demography","dir":"Articles","previous_headings":"Interfaces","what":"Human Demography","title":"Understanding exDE","text":"exDE provides built-support human demography: births handled object deaths, migration, aging handled configuration dHdt object.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"exogenous-forcing","dir":"Articles","previous_headings":"","what":"Exogenous Forcing","title":"Understanding exDE","text":"software designed handle exogenous forcing weather variables.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/Understanding_exDE.html","id":"setup-solving","dir":"Articles","previous_headings":"","what":"Setup & Solving","title":"Understanding exDE","text":"set functions developed basic setup related vignette, Ross-Maconald model presented modular form","code":""},{"path":[]},{"path":"https://dd-harp.github.io/exDE/articles/adult_GeRM.html","id":"delay-differential-equations","dir":"Articles","previous_headings":"Differential Equations","what":"Delay Differential Equations","title":"The Generalized Ross-Macdonald Adult Mosquito Model","text":"equations naturally implemented exDE::dMYZdt.RM_dde, can also implemented closely related set odes using exDE::dMYZdt.RM_ode (see ). \\[ \\dot{M} = \\Lambda - \\Omega\\cdot M \\] \\[ \\dot{G} = \\mbox{diag}(f) \\cdot (M-G) - \\nu G -  \\Omega \\cdot G \\] \\[ \\dot{Y} = \\mbox{diag}(fq\\kappa) \\cdot (M-Y) - \\Omega \\cdot Y \\] \\[ \\dot{Z} = e^{-\\Omega \\tau} \\cdot \\mbox{diag}(fq\\kappa_{t-\\tau}) \\cdot (M_{t-\\tau}-Y_{t-\\tau}) - \\Omega \\cdot Z \\] Recall mosquito demography matrix describing mortality dispersal given : \\[ \\Omega =  \\mbox{diag(g)} + \\left(- {\\cal K}\\right) \\cdot \\mbox{diag}(\\sigma) \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_GeRM.html","id":"ordinary-differential-equations","dir":"Articles","previous_headings":"Differential Equations","what":"Ordinary Differential Equations","title":"The Generalized Ross-Macdonald Adult Mosquito Model","text":"following, equation solved exDE::dMYZdt.RM_ode. system ODEs except equation giving rate change infectious mosquito density, becomes: \\[ \\dot{Z} = e^{-\\Omega \\tau} \\cdot \\mbox{diag}(fq\\kappa) \\cdot (M-Y) - \\Omega \\cdot Z \\] resulting set equations similar spirit simple model presented Smith & McKenzie (2004) mortality dispersal EIP accounted , time lag . transient dynamics ODE model equal DDE model, equilibrium values, numerical work requiring finding equilibrium points, faster ODE model can safely substituted.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_GeRM.html","id":"equilibrium-solutions","dir":"Articles","previous_headings":"","what":"Equilibrium solutions","title":"The Generalized Ross-Macdonald Adult Mosquito Model","text":"two logical ways begin solving non-trivial equilibrium. first assumes \\(\\Lambda\\) known, implies good knowledge mosquito ecology. second assumes \\(Z\\) known, implies knowledge biting rate human population. show .","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_GeRM.html","id":"starting-with-lambda","dir":"Articles","previous_headings":"Equilibrium solutions","what":"Starting with \\(\\Lambda\\)","title":"The Generalized Ross-Macdonald Adult Mosquito Model","text":"Piven \\(\\Lambda\\) can solve: \\[ M = \\Omega^{-1} \\cdot \\Lambda \\] given \\(M\\) set \\(\\dot{Y}\\) zero factor \\(Y\\) get: \\[ Y = (\\mbox{diag}(fq\\kappa) + \\Omega)^{-1} \\cdot \\mbox{diag}(fq\\kappa) \\cdot M \\] set \\(\\dot{Z}\\) zero get: \\[ Z = \\Omega^{-1} \\cdot e^{-\\Omega \\tau} \\cdot \\mbox{diag}(fq\\kappa) \\cdot (M-Y) \\] dynamics \\(P\\) independent infection dynamics, can solve given \\(M\\) : \\[ G = (\\Omega + \\mbox{diag}(f+\\nu))^{-1} \\cdot \\mbox{diag}(f) \\cdot M \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_GeRM.html","id":"starting-with-z","dir":"Articles","previous_headings":"Equilibrium solutions","what":"Starting with \\(Z\\)","title":"The Generalized Ross-Macdonald Adult Mosquito Model","text":"common start estimate \\(Z\\), perhaps derived estimated EIR (entomological inoculation rate). Piven \\(Z\\), can calculate state variables \\(\\Lambda\\). numerical implementation, note \\((e^{-\\Omega\\tau})^{-1} = e^{\\Omega\\tau}\\). \\[ M-Y = \\mbox{diag}(1/fq\\kappa) \\cdot (e^{-\\Omega\\tau})^{-1} \\cdot \\Omega \\cdot Z \\] \\[ Y = \\Omega^{-1} \\cdot \\mbox{diag}(fq\\kappa) \\cdot (M-Y) \\] \\[ M = (M - Y) + Y \\] \\[ \\Lambda = \\Omega \\cdot M \\] can use equation \\(G\\) .","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_GeRM.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"The Generalized Ross-Macdonald Adult Mosquito Model","text":"show example starting solving model equilibrium. Please note runs adult mosquito model users read fully worked example run full simulation.","code":"library(exDE) library(expm) library(deSolve) library(data.table) library(ggplot2) nPatches <- 3 params <- make_parameters_xde(\"ode\") params$nPatches <- nPatches params$nVectors =1"},{"path":"https://dd-harp.github.io/exDE/articles/adult_GeRM.html","id":"the-ross-macdonald-parameterization","dir":"Articles","previous_headings":"Example","what":"The Ross-Macdonald Parameterization","title":"The Generalized Ross-Macdonald Adult Mosquito Model","text":"RM model, can set parameters simulation 3 patches. Now set values \\(\\kappa\\) \\(\\Lambda\\) solve equilibrium values. use exDE::make_inits_MYZ_RM store initial values. equations implemented compute \\(\\Upsilon\\) dynamically, attach Upsilon initial values: set indices exDE::make_indices. can set initial conditions vector use deSolve::ode solve model. Normally values computed within exDE::xDE_diffeqn. , set local version: output plotted . flat lines shown verification steady state solutions computed match steady states computed solving equations:","code":"f <- 0.3 q <- 0.9 g <- 1/20 sigma <- 1/10 eip <- 11 nu <- 1/2 eggsPerBatch <- 30  calK <- matrix(0, nPatches, nPatches) calK[1, 2:3] <- c(0.2, 0.8) calK[2, c(1,3)] <- c(0.5, 0.5) calK[3, 1:2] <- c(0.7, 0.3) calK <- t(calK)  Omega <- make_Omega(g, sigma, calK, nPatches) Upsilon <- expm::expm(-Omega * eip)  params = make_parameters_MYZ_GeRM(params, g, sigma, f, q, nu, eggsPerBatch, eip, calK, solve_as = \"ode\") kappa <- c(0.1, 0.075, 0.025) Lambda <- c(5, 10, 8)  Omega_inv <- solve(Omega)  M_eq <- as.vector(Omega_inv %*% Lambda) G_eq <- as.vector(solve(diag(f+nu, nPatches) + Omega) %*% diag(f, nPatches) %*% M_eq) Y_eq <- as.vector(solve(diag(f*q*kappa) + Omega) %*% diag(f*q*kappa) %*% M_eq) Z_eq <- as.vector(Omega_inv %*% Upsilon %*% diag(f*q*kappa) %*% (M_eq - Y_eq)) params = make_inits_MYZ_GeRM_ode(pars = params,                               M0 = M_eq, G0 = G_eq, Y0 = Y_eq, Z0 = Z_eq) params$Lambda[[1]] = Lambda  params$kappa[[1]] = kappa params = make_indices(params) y0 = get_inits_MYZ(params, 1)    dMYZdt_local = function(t, y, pars, s=1) {   list(dMYZdt(t, y, pars, s)) }  out <- deSolve::ode(y = y0, times = 0:50, dMYZdt_local, parms=params,                      method = 'lsoda', s=1) colnames(out)[params$ix$MYZ[[1]]$M_ix+1] <- paste0('M_', 1:params$nPatches) colnames(out)[params$ix$MYZ[[1]]$G_ix+1] <- paste0('G_', 1:params$nPatches) colnames(out)[params$ix$MYZ[[1]]$Y_ix+1] <- paste0('Y_', 1:params$nPatches) colnames(out)[params$ix$MYZ[[1]]$Z_ix+1] <- paste0('Z_', 1:params$nPatches)  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Patch\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Patch)) +   geom_line() +   facet_wrap(. ~ Component, scales = 'free') +   theme_bw()"},{"path":[]},{"path":"https://dd-harp.github.io/exDE/articles/adult_RM.html","id":"delay-differential-equations","dir":"Articles","previous_headings":"Differential Equations","what":"Delay Differential Equations","title":"A Ross-Macdonald Adult Mosquito Model","text":"equations naturally implemented exDE::dMYZdt.RM_dde, can also implemented closely related set odes using exDE::dMYZdt.RM_ode (see ). \\[ \\dot{M} = \\Lambda - \\Omega\\cdot M \\] \\[ \\dot{P} = \\mbox{diag}(f) \\cdot (M-P) -  \\Omega \\cdot P \\] \\[ \\dot{Y} = \\mbox{diag}(fq\\kappa) \\cdot (M-Y) - \\Omega \\cdot Y \\] \\[ \\dot{Z} = e^{-\\Omega \\tau} \\cdot \\mbox{diag}(fq\\kappa_{t-\\tau}) \\cdot (M_{t-\\tau}-Y_{t-\\tau}) - \\Omega \\cdot Z \\] Recall mosquito demography matrix describing mortality dispersal given : \\[ \\Omega =  \\mbox{diag(g)} + \\left(- {\\cal K}\\right) \\cdot \\mbox{diag}(\\sigma) \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_RM.html","id":"ordinary-differential-equations","dir":"Articles","previous_headings":"Differential Equations","what":"Ordinary Differential Equations","title":"A Ross-Macdonald Adult Mosquito Model","text":"following, equation solved exDE::dMYZdt.RM_ode. system ODEs except equation giving rate change infectious mosquito density, becomes: \\[ \\dot{Z} = e^{-\\Omega \\tau} \\cdot \\mbox{diag}(fq\\kappa) \\cdot (M-Y) - \\Omega \\cdot Z \\] resulting set equations similar spirit simple model presented Smith & McKenzie (2004)2. mortality dispersal EIP accounted , time lag . transient dynamics ODE model equal DDE model, equilibrium values, numerical work requiring finding equilibrium points, faster ODE model can safely substituted.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_RM.html","id":"equilibrium-solutions","dir":"Articles","previous_headings":"","what":"Equilibrium solutions","title":"A Ross-Macdonald Adult Mosquito Model","text":"two logical ways begin solving non-trivial equilibrium. first assumes \\(\\Lambda\\) known, implies good knowledge mosquito ecology. second assumes \\(Z\\) known, implies knowledge biting rate human population. show .","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_RM.html","id":"starting-with-lambda","dir":"Articles","previous_headings":"Equilibrium solutions","what":"Starting with \\(\\Lambda\\)","title":"A Ross-Macdonald Adult Mosquito Model","text":"Piven \\(\\Lambda\\) can solve: \\[ M = \\Omega^{-1} \\cdot \\Lambda \\] given \\(M\\) set \\(\\dot{Y}\\) zero factor \\(Y\\) get: \\[ Y = (\\mbox{diag}(fq\\kappa) + \\Omega)^{-1} \\cdot \\mbox{diag}(fq\\kappa) \\cdot M \\] set \\(\\dot{Z}\\) zero get: \\[ Z = \\Omega^{-1} \\cdot e^{-\\Omega \\tau} \\cdot \\mbox{diag}(fq\\kappa) \\cdot (M-Y) \\] dynamics \\(P\\) independent infection dynamics, can solve given \\(M\\) : \\[ P = (\\Omega + \\mbox{diag}(f))^{-1} \\cdot \\mbox{diag}(f) \\cdot M \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_RM.html","id":"starting-with-z","dir":"Articles","previous_headings":"Equilibrium solutions","what":"Starting with \\(Z\\)","title":"A Ross-Macdonald Adult Mosquito Model","text":"common start estimate \\(Z\\), perhaps derived estimated EIR (entomological inoculation rate). Piven \\(Z\\), can calculate state variables \\(\\Lambda\\). numerical implementation, note \\((e^{-\\Omega\\tau})^{-1} = e^{\\Omega\\tau}\\). \\[ M-Y = \\mbox{diag}(1/fq\\kappa) \\cdot (e^{-\\Omega\\tau})^{-1} \\cdot \\Omega \\cdot Z \\] \\[ Y = \\Omega^{-1} \\cdot \\mbox{diag}(fq\\kappa) \\cdot (M-Y) \\] \\[ M = (M - Y) + Y \\] \\[ \\Lambda = \\Omega \\cdot M \\] can use equation \\(P\\) .","code":""},{"path":"https://dd-harp.github.io/exDE/articles/adult_RM.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"A Ross-Macdonald Adult Mosquito Model","text":"show example starting solving model equilibrium. Please note runs adult mosquito model users read fully worked example run full simulation.","code":"library(exDE) library(expm) library(deSolve) library(data.table) library(ggplot2)"},{"path":"https://dd-harp.github.io/exDE/articles/adult_RM.html","id":"the-long-way","dir":"Articles","previous_headings":"Example","what":"The long way","title":"A Ross-Macdonald Adult Mosquito Model","text":"set parameters simulation 3 patches. Now set parameter environment correct class using exDE::make_parameters_MYZ_RM, noting solving ode. Now set values \\(\\kappa\\) \\(\\Lambda\\) solve equilibrium values. use exDE::make_inits_MYZ_RM store initial values. equations implemented compute \\(\\Upsilon\\) dynamically, attach Upsilon initial values: set indices exDE::make_indices. can set initial conditions vector use deSolve::ode solve model. Normally values computed within exDE::xDE_diffeqn. , set local version: output plotted . flat lines shown verification steady state solutions computed match steady states computed solving equations:","code":"nPatches <- 3 f <- 0.3 q <- 0.9 g <- 1/20 sigma <- 1/10 eip <- 11 nu <- 1/2 eggsPerBatch <- 30  calK <- matrix(0, nPatches, nPatches) calK[1, 2:3] <- c(0.2, 0.8) calK[2, c(1,3)] <- c(0.5, 0.5) calK[3, 1:2] <- c(0.7, 0.3) calK <- t(calK)  Omega <- make_Omega(g, sigma, calK, nPatches) Upsilon <- expm::expm(-Omega * eip) params <- list(nPatches = nPatches)  params = make_parameters_MYZ_RM(params,                                  g = g, sigma = sigma, calK = calK,                                  f = f, q = q,                                  nu = nu, eggsPerBatch = eggsPerBatch,                                  eip = eip, solve_as = 'ode') kappa <- c(0.1, 0.075, 0.025) Lambda <- c(5, 10, 8)  Omega_inv <- solve(Omega)  M_eq <- as.vector(Omega_inv %*% Lambda) P_eq <- as.vector(solve(diag(f, nPatches) + Omega) %*% diag(f, nPatches) %*% M_eq) Y_eq <- as.vector(solve(diag(f*q*kappa) + Omega) %*% diag(f*q*kappa) %*% M_eq) Z_eq <- as.vector(Omega_inv %*% Upsilon %*% diag(f*q*kappa) %*% (M_eq - Y_eq)) params = make_inits_MYZ_RM_ode(pars = params,                               M0 = M_eq, P0 = P_eq, Y0 = Y_eq, Z0 = Z_eq) params$max_ix = 0  params = make_indices(params) params$nHosts = 0 y0 = get_inits_MYZ(params, 1)    dMYZdt_local = func=function(t, y, pars, Lambda, kappa, s) {   pars$Lambda[[s]] = Lambda   pars$kappa[[s]] = kappa    list(dMYZdt(t, y, pars, s)) }  out <- deSolve::ode(y = y0, times = 0:50, dMYZdt_local, parms=params,                      method = 'lsoda', Lambda = Lambda, kappa = kappa, s=1)  out1 <- out colnames(out)[params$MYZpar$M_ix+1] <- paste0('M_', 1:params$nPatches) colnames(out)[params$MYZpar$P_ix+1] <- paste0('P_', 1:params$nPatches) colnames(out)[params$MYZpar$Y_ix+1] <- paste0('Y_', 1:params$nPatches) colnames(out)[params$MYZpar$Z_ix+1] <- paste0('Z_', 1:params$nPatches)  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Patch\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Patch)) +   geom_line() +   facet_wrap(. ~ Component, scales = 'free') +   theme_bw()"},{"path":"https://dd-harp.github.io/exDE/articles/adult_RM.html","id":"setup-utilities","dir":"Articles","previous_headings":"Example","what":"Setup Utilities","title":"A Ross-Macdonald Adult Mosquito Model","text":"vignette , set function solve differential equation. hope helps end user understand exDE works hood, point exDE lower costs building, analyzing, using models. functionality exDE can handle case – can set solve model using built-setup utilities. Learning use utilities makes easy set models without learn internals. set model parameters , make three list named parameters values. also attach list initial values want use, applicable. Ross-Macdonald adult mosquito model, attach parameter values: one dynamical components configurable trace algorithm computes derivatives, passes output parameter (see human-trace.R. configure Xpar, attach values kappa list: Similarly, configure trace algorithm aquatic mosquitoes (see aquatic-trace.R). set model, call xde_setup nPatches set 3 MYZname set “RM” run Ross-Macdonald model adult mosquitoes; pass options, write MYZopts = MYZo; finally, dispersal matrix calK passed calK=calK Xname set “trace” run trace module human infection dynamics Lname set “trace” run trace module aquatic mosquitoes Otherwise, setup takes care internals: Now, can solve equations using xde_solve compare output got . identical, two objects identical, can simply add absolute value differences:","code":"MYZo = list(   f = 0.3, q = 0.9, g = 1/20, sigma = 1/10,   eip = 11, nu = 1/2, eggsPerBatch = 30,   solve_as = \"ode\",    M0 = M_eq, P0 = P_eq, Y0 = Y_eq, Z0 = Z_eq ) Xo = list(kappa =  c(0.1, 0.075, 0.025)) Lo = list(Lambda = c(5, 10, 8)) xde_setup(MYZname = \"RM\", Xname = \"trace\", Lname = \"trace\",       nPatches=3, calK=calK, membership = c(1:3),      residence = c(1:3), HPop = rep(1, 3),     MYZopts = MYZo, Xopts = Xo, Lopts = Lo) -> MYZeg xde_solve(MYZeg, Tmax=50, dt=1) -> MYZeg  out2 <- MYZeg$outputs$orbits$deout sum(abs(out1-out2))==0  #> [1] TRUE"},{"path":"https://dd-harp.github.io/exDE/articles/aqua_basic.html","id":"differential-equations","dir":"Articles","previous_headings":"","what":"Differential Equations","title":"Basic Competition Aquatic Mosquito Model","text":"Given \\(\\Lambda\\) egg laying rate adult mosquito population formulate solve dynamical model aquatic mosquitoes give emergence rate. However, example simply use trace-based (forced) emergence model, \\(\\Lambda\\) completely specifies aquatic mosquitoes. simplest model aquatic (immature) mosquito dynamics negative feedback (density dependence) : \\[ \\dot{L} = \\eta - (\\psi+\\phi+\\theta L)L \\] equations allow number larval habitats \\(l\\) differ \\(p\\), general emergence rate given : \\[ \\Lambda = \\mathcal{N}\\cdot \\alpha \\] \\(\\mathcal{N}\\) \\(p\\times l\\) matrix \\(\\alpha\\) length \\(l\\) column vector given : \\[ \\alpha = \\psi L \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/aqua_basic.html","id":"equilibrium-solutions","dir":"Articles","previous_headings":"","what":"Equilibrium solutions","title":"Basic Competition Aquatic Mosquito Model","text":"general, know value \\(\\Lambda\\) equilibrium can solve \\(L\\) directly using two equations. can consider \\(\\theta\\), strength density dependence unknown solve : \\[ \\theta = (\\eta - \\psi L - \\phi L) / L^2 \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/aqua_basic.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"Basic Competition Aquatic Mosquito Model","text":"","code":"library(exDE) library(deSolve) library(data.table) library(ggplot2)"},{"path":"https://dd-harp.github.io/exDE/articles/aqua_basic.html","id":"the-long-way","dir":"Articles","previous_headings":"Example","what":"The long way","title":"Basic Competition Aquatic Mosquito Model","text":"run simple example 3 aquatic habitats equilibrium. use exDE::make_parameters_L_basic set parameters. Please note runs aquatic mosquito component users read fully worked example run full simulation.","code":"nHabitats <- 3 alpha <- c(10, 50, 20) eta <- c(250, 500, 170) psi <- 1/10 phi <- 1/12 L <- alpha/psi theta <- (eta - psi*L - phi*L)/(L^2) params <- make_parameters_xde()  params$nHabitats = nHabitats params$eggs_laid = list()  params$eggs_laid[[1]] = eta  F_eta = function(t, pars){   pars$eggs_laid[[1]] }  params = make_parameters_L_basic(pars = params, psi = psi, phi = phi, theta = theta) params = make_inits_L_basic(params, L0=L)  params = make_indices(params) xDE_aquatic = function(t, y, pars, F_eta) {   pars$eggs_laid[[1]] <- F_eta(t, pars)   dL <- dLdt(t, y, pars, 1)   return(list(c(dL))) } y0 <- get_inits(params)   out <- deSolve::ode(y = y0, times = 0:50, xDE_aquatic, parms = params, method = 'lsoda', F_eta = F_eta)  out1 <- out colnames(out)[params$L_ix+1] <- paste0('L_', 1:params$nHabitats)  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Patch\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Patch)) +   geom_line() +   theme_bw()"},{"path":"https://dd-harp.github.io/exDE/articles/aqua_basic.html","id":"using-setup","dir":"Articles","previous_headings":"Example","what":"Using Setup","title":"Basic Competition Aquatic Mosquito Model","text":"function xde_setup_aquatic sets model includes aquatic dynamics, solved using xde_solve.aqua. setup functions simpler xde_setup come constrained choices. user can configure aquatic model (trace wouldn’t make much sense), uses Gtrace force egg laying. configure aquatic model: Lo list parameter values attached. use MYZ model Gtrace configure egg laying.","code":"Lo = list(   psi = 1/10,    phi = 1/12 ) alpha = c(10, 50, 20) Lo$L0 = with(Lo, alpha/psi)  Lo$theta = with(Lo, (eta - psi*L0 - phi*L0)/(L0^2)) Mo = list(Gm = c(250, 500, 170)) xde_setup_aquatic(nHabitats = 3, Lname = \"basic\", Lopts = Lo, MYZopts = Mo) -> aqbasic xde_solve(aqbasic, Tmax=50, dt=1)$output$orbits$deout -> out2 sum(abs(out1-out2)) == 0 #> [1] TRUE"},{"path":"https://dd-harp.github.io/exDE/articles/aqua_trace.html","id":"a-forced-model","dir":"Articles","previous_headings":"","what":"A forced model","title":"Trace (exogenously forced) Aquatic Mosquito Model","text":"null model aquatic mosquito dynamics; endogenous dynamics model simply specified Lambda, rate adult mosquitoes spontaneously emerge aquatic habitats. show example, taken package tests, using trace-based aquatic model keep adult mosquito model equilibrium using unequal numbers aquatic habitats per patch.","code":"library(exDE) library(MASS) library(expm) library(deSolve) library(data.table) library(ggplot2)"},{"path":"https://dd-harp.github.io/exDE/articles/aqua_trace.html","id":"the-long-way","dir":"Articles","previous_headings":"A forced model","what":"The Long Way","title":"Trace (exogenously forced) Aquatic Mosquito Model","text":"First, set parameter values. Next, calculate equilibrium values following Ross-Macdonald vignette. use \\(\\mathcal{N}\\) \\(\\mathcal{U}\\) describe aquatic habitats dispersed amongst patches, mosquitoes patch disperse eggs habitat, respectively. Please note unequal numbers aquatic habitats patches, use MASS::ginv compute generalized inverse \\(\\mathcal{N}\\) get \\(\\alpha\\) required equilibrium. Now set model. Please see Ross-Macdonald vignette details adult model. use alpha Lambda parameter forced emergence model, exDE::make_parameters_L_trace. , running full transmission model, must use exDE::MosquitoBehavior pass equilibrium values bionomic parameters exDE::xDE_diffeqn_mosy.","code":"nPatches <- 3 nHabitats <- 4 f <- 0.3 q <- 0.9 g <- 1/20 sigma <- 1/10 eip <- 11 nu <- 1/2 eggsPerBatch <- 30  calN <- matrix(0, nPatches, nHabitats) calN[1,1] <- 1 calN[2,2] <- 1 calN[3,3] <- 1 calN[3,4] <- 1  calU <- matrix(0, nHabitats, nPatches) calU[1,1] <- 1 calU[2,2] <- 1 calU[3:4,3] <- 0.5  calK <- matrix(0, nPatches, nPatches) calK[1, 2:3] <- c(0.2, 0.8) calK[2, c(1,3)] <- c(0.5, 0.5) calK[3, 1:2] <- c(0.7, 0.3) calK <- t(calK)  Omega <- make_Omega(g, sigma, calK, nPatches) Upsilon <- expm::expm(-Omega * eip)  kappa <- c(0.1, 0.075, 0.025) Lambda <- c(5, 10, 8) # equilibrium solutions Omega_inv <- solve(Omega)  M_eq <- as.vector(Omega_inv %*% Lambda) P_eq <- as.vector(solve(diag(f, nPatches) + Omega) %*% diag(f, nPatches) %*% M_eq)  # the \"Lambda\" for the dLdt model alpha <- as.vector(ginv(calN) %*% Lambda) params = make_parameters_xde() class(params$BFpar) <- \"static\" class(params$EGGpar) <- \"simple\" params$nVectors = 1  params$nHosts = 1  params$nPatches = nPatches params$nHabitats = nHabitats params$calU[[1]] = calU params$calN = calN   # ODE params$beta = beta params = make_parameters_L_trace(pars = params, Lambda = alpha) params = make_parameters_MYZ_basicM(pars = params, g = g, sigma = sigma, calK = calK, f = f, q = q, nu = nu, eggsPerBatch = eggsPerBatch) params = make_inits_MYZ_basicM(params, M0=M_eq, P0=P_eq)  params = make_indices(params) y0 <- rep(0, params$max_ix) y0[params$ix$MYZ[[1]]$M_ix] <- M_eq y0[params$ix$MYZ[[1]]$P_ix] <- P_eq  out <- deSolve::ode(y = y0, times = 0:50, func = xDE_diffeqn_mosy, parms = params, method = 'lsoda') out1 <- out colnames(out)[params$ix$MYZ[[1]]$M_ix+1] <- paste0('M_', 1:params$nPatches) colnames(out)[params$ix$MYZ[[1]]$P_ix+1] <- paste0('P_', 1:params$nPatches)  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Patch\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Patch)) +   geom_line() +   facet_wrap(. ~ Component, scales = 'free') +   theme_bw()"},{"path":"https://dd-harp.github.io/exDE/articles/aqua_trace.html","id":"using-setup","dir":"Articles","previous_headings":"A forced model","what":"Using Setup","title":"Trace (exogenously forced) Aquatic Mosquito Model","text":"","code":"Lo = list(   Lambda = alpha  ) MYZo = list(   f = 0.3,   q = 0.9,   g = 1/20,   sigma = 1/10,   eip = 11,   nu = 1/2,   eggsPerBatch = 30,   M0=M_eq,   P0=P_eq ) xde_setup_mosy(MYZname = \"basicM\", Lname = \"trace\",                 nPatches = 3, membership = c(1,2,3,3),                 MYZopts = MYZo, calK = calK, Lopts = Lo,                 kappa = c(0.1, 0.075, 0.025))->mosy1 xde_solve(mosy1,Tmax=50,dt=1)$outputs$orbits$deout -> out2 sum(out2-out1) #> [1] 0"},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"5-3-4 Example","text":"show setup, solve, analyze models mosquito-borne pathogen transmission dynamics control using modular software. vignette designed explain modular notation constructing model five aquatic habitats (\\(l=5\\)), three patches (\\(p=3\\)), four human population strata (\\(n=4\\)). call 5-3-4.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"diagram","dir":"Articles","previous_headings":"Introduction","what":"Diagram","title":"5-3-4 Example","text":"model 5-3-4 designed illustrate important features framework notation. assume : first three habitats found patch 1; last two patch 2; patch 3 habitats. patch 1 residents; patches 2 3 occupied, two different population strata; Transmission among patches modeled using concept time spent, similar visitation rates used models. strata residency (.e; patch spend time ), stratum allocates time across habitats.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"parameters","dir":"Articles","previous_headings":"","what":"Parameters","title":"5-3-4 Example","text":"already know three important parameters, \\(l\\), \\(p\\) \\(n\\) determined early stages model building. exDE package expects parameters contained list object, containing nHabitats, nPatches, nStrata correspond l, p n.","code":"params = make_parameters_xde()  params$nVectors = 1 params$nHosts = 1 params$nHabitats = 5 params$nPatches = 3 params$nStrata = 4"},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"aquatic-habitat-membership-matrix","dir":"Articles","previous_headings":"Parameters","what":"Aquatic Habitat Membership Matrix","title":"5-3-4 Example","text":"aquatic habitat membership matrix \\(\\mathcal{N}\\) \\(p \\times l\\) matrix mapping aquatic habitats patches contain . attached directly parameters list. \\[\\begin{equation} {\\cal N} = \\left[ \\begin{array}{ccccc} 1 & 1 & 1 & 0 & 0 \\\\ 0 & 0 & 0 & 1 & 1\\\\ 0 & 0 & 0 & 0 & 0\\\\ \\end{array} \\right] \\end{equation}\\]","code":"calN <- matrix(  data = c(1,1,1,0,0,       0,0,0,1,1,       0,0,0,0,0),   nrow = params$nPatches, ncol = params$nHabitats, byrow = TRUE ) params$calN <- calN"},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"egg-dispersal-matrix","dir":"Articles","previous_headings":"Parameters","what":"Egg Dispersal Matrix","title":"5-3-4 Example","text":"egg dispersal matrix \\(\\mathcal{U}\\) \\(l \\times p\\) matrix describing eggs laid adult mosquitoes patch allocated among aquatic habitats patch. also attached directly parameters list. \\[\\begin{equation} {\\cal U} = \\left[ \\begin{array}{ccccc} .7 & 0 & 0\\\\ .2 & 0 & 0\\\\ .1 & 0 & 0\\\\ 0 & .8 & 0\\\\ 0 & .2 & 0\\\\ \\end{array} \\right] \\end{equation}\\]","code":"xi <- matrix(c(.7, .2, .1, .8, .2), 5, 1)  params$EGGpar$searchWts[[1]] <- as.vector(xi) params$calU[[1]]<- t(calN %*% diag(as.vector(xi)))"},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"aquatic-mosquito-parameters","dir":"Articles","previous_headings":"Parameters","what":"Aquatic Mosquito Parameters","title":"5-3-4 Example","text":"simulation, use basic competition model larval dynamics (see ). requires specification three parameters, \\(\\psi\\) (maturation rates), \\(\\phi\\) (density-independent mortality rates), \\(\\theta\\) (density-dependent mortality terms), initial conditions. function exDE::make_parameters_L_basic basic checking input parameters returns list correct class method dispatch. returned list attached main parameter list name Lpar.","code":"L0 <- rep(1, params$nHabitats) psi <- rep(1/8, params$nHabitats) phi <- rep(1/8, params$nHabitats) theta <- c(1/10, 1/20, 1/40, 1/100, 1/10)   params = make_parameters_L_basic(params, psi = psi, phi = phi, theta = theta) params = make_inits_L_basic(params, L0=L0)"},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"adult-mosquito-parameters","dir":"Articles","previous_headings":"Parameters","what":"Adult Mosquito Parameters","title":"5-3-4 Example","text":"use ODE version generalized Ross-Macdonald model (see ). Part specification parameters includes construction mosquito dispersal matrix \\(\\mathcal{K}\\), mosquito demography matrix \\(\\Omega\\). Like aquatic parameters, use exDE::make_parameters_MYZ_RM_ode check parameter types return list correct class method dispatch. attach returned list main parameter list name MYZpar.","code":"g <- 1/12 sigma <- 1/12/2 f <- 1/3 q <- 0.9 nu <- c(1/3,1/3,0)   eggsPerBatch <- 30  eip <- 12   calK <- t(matrix(  c(c(0, .6, .3),    c(.4, 0, .7),    c(.6, .4, 0)), 3, 3))  M0 <- rep(100, params$nPatches) P0 <- rep(10, params$nPatches) Y0 <- rep(1, params$nPatches) Z0 <- rep(0, params$nPatches)  Omega <- make_Omega(g, sigma, calK, params$nPatches) Upsilon <- expm::expm(-Omega*eip)  params = make_parameters_MYZ_RM(pars = params, g = g,                  sigma = sigma, calK=calK,                  eip=eip, f=f, q=q, nu=nu,                  eggsPerBatch=eggsPerBatch,                  solve_as = \"ode\")   params = make_inits_MYZ_RM_ode(params, M0=M0, P0=P0,               Y0=Y0, Z0=Z0)"},{"path":[]},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"mixing","dir":"Articles","previous_headings":"Parameters","what":"Mixing","title":"5-3-4 Example","text":"use static demographic model, assumes constant population size (constant \\(H\\)). model, define four population strata. can describe residency vector describing residence: Although directly used example, create residency membership matrix \\(\\mathcal{J}\\), \\(p \\times n\\) matrix indicating patch human population strata resides . \\[\\begin{equation} {\\cal J} = \\left[ \\begin{array}{cccc} 0 & 0 & 0 & 0 \\\\ 1 & 1 & 0 & 0 \\\\ 0 & 0 & 1 & 1 \\\\ \\end{array} \\right] \\end{equation}\\] create time risk matrix \\(\\Psi\\), \\(p \\times n\\) matrix describing human strata spends time across patches. \\[\\begin{equation} \\Psi= \\left[ \\begin{array}{cccc} 0.01 & .01 & .001 & .001 \\\\ 0.95 & .92 & .04 & .02 \\\\ 0.04 & .02 & .959 & .929 \\\\ \\end{array} \\right] \\end{equation}\\] use basic SIS (Susceptible-Infected-Susceptible) model human component (see ). set like rest components, using exDE::make_parameters_X_SIS make correct return type, attached parameter list name Xpar.","code":"H <- matrix(c(10,90, 100, 900), 4, 1) params = setup_Hpar_static(params, 1, HPop=H) residence = c(2,2,3,3) searchWtsH = c(1,1,1,1) params = setup_BloodFeeding(params, 1, 1, residence=residence, searchWts=searchWtsH) calJ <- t(matrix(  c(c(0,0,0,0),   c(1,1,0,0),   c(0,0,1,1)), 4, 3 )) TaR <- t(matrix(  c(c(0.01,0.01,0.001,0.001),   c(.95,.92,.04,.02),   c(.04,.02,.959,.929)), 4, 3 )) params$BFpar$TaR[[1]][[1]] <- TaR I0 <- as.vector(0.2*H) r <- 1/200 b <- 0.55 c <- c(0.1, .02, .1, .02)  params = make_parameters_X_SIS(pars = params, b = b, c = c, r = r) params = make_inits_X_SIS(params, S0 = H-I0, I0=I0)"},{"path":[]},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"initial-conditions","dir":"Articles","previous_headings":"Simulation, the Long Way","what":"Initial Conditions","title":"5-3-4 Example","text":"parameters 5-3-4 specified, can generate indices model attach parameter list. Now can set initial conditions model.","code":"params = make_indices(params) y0 = get_inits(params) params <- EggLaying(0, y0, params)"},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"numerical-solution","dir":"Articles","previous_headings":"Simulation, the Long Way","what":"Numerical Solution","title":"5-3-4 Example","text":"Now can pass vector initial conditions, y, parameter list params, function exDE::xDE_diffeqn differential equation solvers deSolve::ode generate numerical trajectory. classes Xpar, MYZpar, Lpar params ensure right methods invoked (dispatched) solve model.","code":"out <- deSolve::ode(y = y0, times = 0:365,                      func = xDE_diffeqn, parms = params, method = \"lsoda\") out1 <- out"},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"plot-output","dir":"Articles","previous_headings":"Simulation, the Long Way","what":"Plot Output","title":"5-3-4 Example","text":"small amount data wrangling made easier data.table package, can plot output.","code":"colnames(out)[params$ix$L[[1]]$L_ix+1] <- paste0('L_', 1:params$nHabitats) colnames(out)[params$ix$MYZ[[1]]$M_ix+1] <- paste0('M_', 1:params$nPatches) colnames(out)[params$ix$MYZ[[1]]$P_ix+1] <- paste0('P_', 1:params$nPatches) colnames(out)[params$ix$MYZ[[1]]$Y_ix+1] <- paste0('Y_', 1:params$nPatches) colnames(out)[params$ix$MYZ[[1]]$Z_ix+1] <- paste0('Z_', 1:params$nPatches) colnames(out)[params$ix$X[[1]]$X_ix+1] <- paste0('X_', 1:params$nStrata)  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Stratification\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Stratification)) +  geom_line() +  facet_wrap(. ~ Component, scales = 'free') +  theme_bw()"},{"path":"https://dd-harp.github.io/exDE/articles/ex_534.html","id":"using-setup","dir":"Articles","previous_headings":"","what":"Using Setup","title":"5-3-4 Example","text":"create lists parameters values: solve take differences check: Interestingly, differences small:","code":"MYZo = list(  solve_as = \"ode\",   g = 1/12, sigma = 1/12/2,  f = 1/3, q=0.9, nu=c(1/3,1/3,0),  eggsPerBatch = 30,   eip = 12,   M0 = 100,  P0 = 10,  Y0 = 1, Z0 = 0  ) Lo = list(  L0 = 1,  psi = 1/8, phi = 1/8,   theta = c(1/10, 1/20, 1/40, 1/100, 1/10)  ) Xo = list(  I0 = as.vector(0.2*H),  r = 1/200,  b = 0.55,  c = c(0.1, .02, .1, .02) ) EIPo <- list(eip=12) xde_setup(\"mod534\", \"RM\", \"SIS\", \"basic\",                    nPatches = 3, HPop=c(10, 90, 100, 900),                    membership=c(1,1,1,2,2), EIPopts = EIPo,                   MYZopts=MYZo, calK=calK, Xopts=Xo,                    residence=c(2,2,3,3), searchB=searchWtsH,                    TimeSpent=TaR, searchQ = c(7,2,1,8,2), Lopts = Lo) -> mod534 mod534 <- xde_solve(mod534,Tmax=365,dt=1) mod534$outputs$orbits$deout -> out2 approx_equal(tail(out2, 1), tail(out1,1), tol = 1e-5) #>        time   L1   L2   L3   L4   L5 MYZ1 MYZ2 MYZ3 MYZ4 MYZ5 MYZ6 MYZ7 MYZ8 #> [366,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #>        MYZ9 MYZ10 MYZ11 MYZ12   X1   X2   X3   X4   X5   X6   X7   X8 #> [366,] TRUE  TRUE  TRUE  TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE"},{"path":"https://dd-harp.github.io/exDE/articles/human_hmoi.html","id":"differential-equations","dir":"Articles","previous_headings":"","what":"Differential Equations","title":"Hybrid MoI (Multiplicity of Infection) Human Model","text":"equations follows: \\[ \\dot{m_{1}} = h - r_{1}m_{1} \\] \\[ \\dot{m_{2}} = h - r_{2}m_{2} \\] \\(h = b EIR\\), force infection. Prevalence can calculated MoI values : \\[ x_{1} = 1-e^{-m_{1}} \\] \\[ x_{2} = 1-e^{-m_{2}} \\] net infectious probability mosquitoes therefore given : \\[ x = c_{2}x_{2} + c_{1}(x_{1}-x_{2}) \\] \\(c_{1}\\) infectiousness inapparent infections, \\(c_{2}\\) infectiousness patent infections.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/human_hmoi.html","id":"equilibrium-solutions","dir":"Articles","previous_headings":"","what":"Equilibrium solutions","title":"Hybrid MoI (Multiplicity of Infection) Human Model","text":"One way proceed assume \\(m_{2}\\) known, models MoI patent (observable) infections. : \\[ h = r_{2}/m_{2} \\] \\[ m_{1} = h/r_{1} \\] can use calculate net infectious probability, \\(\\kappa = \\beta^{\\top} \\cdot x\\), allowing equilibrium solutions model feed components.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/human_hmoi.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"Hybrid MoI (Multiplicity of Infection) Human Model","text":"run simple example 3 population strata equilibrium. use exDE::make_parameters_X_hMoI set parameters. Please note runs human population component users read fully worked example run full simulation. use null (constant) model human demography (\\(H\\) constant time). \\(H\\) appear equations , must specified model bloodfeeding (\\(\\beta\\)) relies \\(H\\) compute consistent values.","code":"library(exDE) library(deSolve) library(data.table) library(ggplot2)"},{"path":"https://dd-harp.github.io/exDE/articles/human_hmoi.html","id":"the-long-way","dir":"Articles","previous_headings":"","what":"The Long Way","title":"Hybrid MoI (Multiplicity of Infection) Human Model","text":", build model step--step.","code":"nStrata <- 3 H <- c(100, 500, 250) residence = rep(1,3)  searchWtsH = rep(1,3)  b <- 0.55 c1 <- 0.05 c2 <- 0.25 r1 <- 1/250 r2 <- 1/50 TaR <- matrix(data = 1, nrow = 1, ncol = nStrata)  m20 <- 1.5 h <- r2*m20 m10 <- h/r1  EIR <- h/b params <- make_parameters_xde() params$nStrata = nStrata params$nVectors = 1  params$nHosts = 1 params$nPatches = 1  params$eir = rep(EIR, 3) params$EIR = list()  F_eir = function(t, pars){   pars$EIR[[1]] = pars$eir }  params = make_parameters_demography_null(pars = params, H=H)   params = setup_BloodFeeding(params, 1, 1, residence=residence, searchWts=searchWtsH)  params$BFpar$TaR[[1]][[1]]=TaR params = make_parameters_X_hMoI(pars = params, b = b, c1 = c1, c2 = c2, r1 = r1, r2 = r2) params = make_inits_X_hMoI(pars = params, rep(m10, nStrata), rep(m20, nStrata))  params = make_indices(params) y0 <- get_inits(params)  out <- deSolve::ode(y = y0, times = c(0, 365), func = xDE_diffeqn_cohort,                      parms = params, method = 'lsoda', F_eir = F_eir)  out1 <- out colnames(out)[params$ix$X[[1]]$m1_ix+1] <- paste0('m1_', 1:params$nStrata) colnames(out)[params$ix$X[[1]]$m2_ix+1] <- paste0('m2_', 1:params$nStrata)  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Strata\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Strata)) +   geom_line() +   facet_wrap(Strata ~ Component, scales = 'free') +   theme_bw()"},{"path":"https://dd-harp.github.io/exDE/articles/human_hmoi.html","id":"using-setup","dir":"Articles","previous_headings":"","what":"Using Setup","title":"Hybrid MoI (Multiplicity of Infection) Human Model","text":"","code":"Xo = list(b=0.55, c1=0.05, c2=0.25, r1=1/250, r2=1/50, m20=1.5) h = with(Xo, r2*m20)  Xo$m10 = with(Xo, h/r1)   Hpop = c(100, 500, 250) h/b #> [1] 0.05454545 fF_eir1 = function(EIR){return(function(t, pars){EIR})}  F_eir1 = fF_eir1(EIR) xde_setup_cohort(F_eir1, Xname=\"hMoI\", HPop=Hpop, Xopts = Xo) ->test_hMoI xde_solve(test_hMoI, 365, 365)$outputs$orbits$deout -> out2 approx_equal(out2, out1) #>      time   X1   X2   X3   X4   X5   X6 #> [1,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [2,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE"},{"path":"https://dd-harp.github.io/exDE/articles/human_sip.html","id":"differential-equations","dir":"Articles","previous_headings":"","what":"Differential Equations","title":"SIP (Susceptible-Infected-Prophylaxis) Human Model","text":"equations follows: \\[ \\dot{X} = \\mbox{diag}((1-\\rho)bEIR)\\cdot (H-X-P) - (r+\\xi)X \\] \\[ \\dot{P} = \\mbox{diag}(\\rho b EIR) \\cdot (H-X-P) + \\xi(H-P) - \\eta P \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/human_sip.html","id":"equilibrium-solutions","dir":"Articles","previous_headings":"","what":"Equilibrium solutions","title":"SIP (Susceptible-Infected-Prophylaxis) Human Model","text":", assume \\(H\\) \\(X\\) known, set \\(\\xi=0\\), solve \\(EIR\\) \\(P\\). \\[ P = \\mbox{diag}(1/\\eta) \\cdot \\mbox{diag}(\\rho/(1-\\rho)) \\cdot rX \\] \\[ EIR = \\mbox{diag}(1/b) \\cdot \\mbox{diag}(1/(1-\\rho)) \\cdot \\left( \\frac{rX}{H-X-P} \\right) \\] Given \\(EIR\\) can solve mosquito population given rise equilibrium values.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/human_sip.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"SIP (Susceptible-Infected-Prophylaxis) Human Model","text":"run simple example 3 population strata equilibrium. use exDE::make_parameters_X_SIP set parameters. Please note runs human population component users read fully worked example run full simulation. use null (constant) model human demography (\\(H\\) constant time).","code":"library(exDE) library(deSolve) library(data.table) library(ggplot2)"},{"path":"https://dd-harp.github.io/exDE/articles/human_sip.html","id":"the-long-way","dir":"Articles","previous_headings":"Example","what":"The Long Way","title":"SIP (Susceptible-Infected-Prophylaxis) Human Model","text":"","code":"nStrata <- 3 H <- c(100, 500, 250) residence <- rep(1,3)  searchWtsH <- rep(1,3)  I <- c(20, 120, 80) b <- 0.55 c <- 0.15 r <- 1/200 eta <- c(1/30, 1/40, 1/35) rho <- c(0.05, 0.1, 0.15) xi <- rep(0, 3)  TaR <- matrix(data = 1,nrow = 1, ncol = nStrata)  P <- diag(1/eta) %*% diag(rho/(1-rho)) %*% (r*I) EIR <- diag(1/b, nStrata) %*% diag(1/(1-rho)) %*% ((r*I)/(H-I-P)) params <- make_parameters_xde() params$nStrata = nStrata params$nPatches = 1  params$nHosts = 1   params$eir = EIR params$EIR = list()  F_eir = function(t, pars){   pars$EIR[[1]] = params$eir }  params = make_parameters_demography_null(pars = params, H=H)   params = setup_BloodFeeding(params, 1, 1, residence=residence, searchWts =searchWtsH)  params$BFpar$TaR[[1]][[1]]=TaR  params = make_parameters_X_SIP(pars = params, b = b, c = c, r = r, rho = rho, eta = eta, xi=xi) params = make_inits_X_SIP(pars = params, H-I-P, I, as.vector(P)) params = make_indices(params) y0 <- get_inits(params) out <- deSolve::ode(y = y0, times = c(0, 365), xDE_diffeqn_cohort, parms = params, method = 'lsoda', F_eir = F_eir)  out1<- out colnames(out)[params$ix$X[[1]]$S_ix+1] <- paste0('S_', 1:params$nStrata) colnames(out)[params$ix$X[[1]]$I_ix+1] <- paste0('I_', 1:params$nStrata) colnames(out)[params$ix$X[[1]]$P_ix+1] <- paste0('P_', 1:params$nStrata)  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Strata\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Strata)) +   geom_line() +   facet_wrap(. ~ Component, scales = 'free') +   theme_bw()"},{"path":"https://dd-harp.github.io/exDE/articles/human_sip.html","id":"using-setup","dir":"Articles","previous_headings":"Example","what":"Using Setup","title":"SIP (Susceptible-Infected-Prophylaxis) Human Model","text":"use xde_setup_cohort must set function F_eir returns value EIR computed :","code":"Xo = list(b=0.55, c=0.15, r=1/200,            eta = c(1/30, 1/40, 1/35), rho = c(0.05, .1, 0.15),            xi = rep(0,3),            I0=I, P0=as.vector(P)) Hpop = c(100, 500, 250) fF_eir1 = function(EIR){return(function(t, pars){EIR})}  F_eir1 = fF_eir1(EIR) xde_setup_cohort(F_eir1, Xname=\"SIP\", HPop=Hpop, Xopts = Xo) -> test_SIP xde_solve(test_SIP, 365, 365)$outputs$orbits$deout -> out2 approx_equal(out2,out1)  #>      time   X1   X2   X3   X4   X5   X6   X7   X8   X9 #> [1,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [2,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE"},{"path":"https://dd-harp.github.io/exDE/articles/human_sis.html","id":"differential-equations","dir":"Articles","previous_headings":"","what":"Differential Equations","title":"SIS (Susceptible-Infected-Susceptible) Human Model","text":"subdivide population susceptible (\\(S\\)) infected infectious (\\(\\)) individuals, total population \\(H = S+.\\) assume force infection (\\(h\\), FoI) linearly proportional EIR: \\(h = b \\times EIR.\\) general form, births (\\(B(H)\\)) deaths (per-capita rate \\(\\mu\\)), generalized SIS dynamics : \\[ \\begin{array}{rl} \\dot{S} &= -h S + rI + B(H) -\\mu S\\\\ \\dot{} &= h S  - rI - \\mu \\end{array} \\] demographic change, SIS model can rewritten single equation: \\[ \\dot{} = h (H-) - rI \\] Even simplified form, assuming population stratified, variables parameter vectors length nStrata.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/human_sis.html","id":"equilibrium-solutions","dir":"Articles","previous_headings":"","what":"Equilibrium Solutions","title":"SIS (Susceptible-Infected-Susceptible) Human Model","text":"typical situation using model \\(H\\) (total population size strata) \\(X\\) (number infectious persons strata) known census survey data. interest find value \\(EIR\\) (Entomological Inoculation Rate) leads prevalence equilibrium. \\[ 0 = \\mbox{diag}(bEIR) \\cdot (H-) - rI \\] \\[ rI = \\mbox{diag}(b) \\cdot \\mbox{diag}(EIR) \\cdot (H-) \\] \\[ \\frac{rI}{H-} = \\mbox{diag}(b) \\cdot \\mbox{diag}(EIR) \\] \\[ \\mbox{diag}(1/b) \\cdot \\left(\\frac{rI}{H-}\\right) = EIR \\] Note final line, \\(EIR\\) column vector dimension \\(n\\) due operations left. element gives per-capita rate individuals population strata receive potentially infectious bites (summing across places visit).","code":""},{"path":"https://dd-harp.github.io/exDE/articles/human_sis.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"SIS (Susceptible-Infected-Susceptible) Human Model","text":"run simple example 3 population strata equilibrium. use exDE::make_parameters_X_SIS set parameters. Please note runs human population component users read fully worked example run full simulation. use null (constant) model human demography (\\(H\\) constant time).","code":"library(exDE) library(deSolve) library(data.table) library(ggplot2)"},{"path":"https://dd-harp.github.io/exDE/articles/human_sis.html","id":"the-long-way","dir":"Articles","previous_headings":"Example","what":"The Long Way","title":"SIS (Susceptible-Infected-Susceptible) Human Model","text":"set systems differential equations, must set values parameters.","code":"nStrata <- 3 H <- c(100, 500, 250) residence <- rep(1,3)  searchWtsH <- rep(1,3)  I <- c(20, 120, 80) b <- rep(0.55, nStrata)  c <- rep(0.15, nStrata)  r <- rep(1/200, nStrata)  TaR <- matrix(data = 1,nrow = 1, ncol = nStrata)  EIR <- diag(1/b, nStrata) %*% ((r*I)/(H-I)) params <- make_parameters_xde() params$nStrata = nStrata params$nPatches = 1 params$nHosts = 1  params$eir = EIR params$EIR = list()   params$eir = as.vector(EIR) F_eir = function(t, pars){   pars$EIR[[1]] = pars$eir }  params = make_parameters_demography_null(pars = params, H=H)   params = setup_BloodFeeding(params, 1, 1, residence=residence, searchWts=searchWtsH)  params$BFpar$TaR[[1]][[1]]=TaR  params = make_parameters_X_SIS(pars = params, b = b, c = c, r = r)  params = make_inits_X_SIS(pars = params, H-I, I)  params = make_indices(params) y0 <- get_inits(params)  out <- deSolve::ode(y = y0, times = c(0, 365), xDE_diffeqn_cohort,                      parms = params, method = 'lsoda', F_eir = F_eir)  out1 <- out colnames(out)[params$ix$X$S_ix+1] <- paste0('S_', 1:params$nStrata) colnames(out)[params$ix$X$I_ix+1] <- paste0('I_', 1:params$nStrata)  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Strata\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Strata)) +   geom_line() +   facet_wrap(. ~ Component, scales = 'free') +   theme_bw()"},{"path":"https://dd-harp.github.io/exDE/articles/human_sis.html","id":"using-setup","dir":"Articles","previous_headings":"Example","what":"Using Setup","title":"SIS (Susceptible-Infected-Susceptible) Human Model","text":"developed utilities setting models. pass parameter values initial values lists: use xde_setup_cohort must set function F_eir returns value EIR computed :","code":"Xo = list(b=0.55, c=0.15, r=1/200, I0 = I) Hpop = c(100, 500, 250) fF_eir1 = function(EIR){return(function(t, pars){EIR})}  F_eir1 = fF_eir1(EIR) xde_setup_cohort(F_eir1, Xname=\"SIS\", HPop=Hpop, Xopts = Xo) -> test_SIS xde_solve(test_SIS, 365, 365)$outputs$orbits$deout -> out2 approx_equal(out2,out1) #>      time   X1   X2   X3   X4   X5   X6 #> [1,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE #> [2,] TRUE TRUE TRUE TRUE TRUE TRUE TRUE"},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Modular Forms for Disease Dynamics","text":"Modular forms disease dynamics stylized ways writing dynamical systems emphasize modular structure. mathematical framework building models malaria dynamics control (mosquito-borne pathogens) described Spatial Dynamics Malaria Transmission, framework implemented exDE. forms describe rewrite models closely resemble implementation exDE, makes possible relate written equations computed code. (Also, see closely related vignette Understanding exDE.)","code":""},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"the-modular-form","dir":"Articles","previous_headings":"","what":"The Modular Form","title":"Modular Forms for Disease Dynamics","text":"illustrate writing Ross-Macdonald model modular form (Figure 1). classical form, model: \\[ \\begin{array}{rl} dX/dt &= b e^{-gn}fq \\frac YH (H-X) - r X \\\\ dY/dt &= c \\frac XH (M-Y) - g Y \\end{array}\\] model explained . Figure 1 - Diagram Ross-Macdonald model written modular form.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"parasite-infection-dynamics-in-humans-cal-x","dir":"Articles","previous_headings":"The Modular Form","what":"Parasite Infection Dynamics in Humans, \\(\\cal X\\)","title":"Modular Forms for Disease Dynamics","text":"equation describing human infections written following way: \\[ dI/dt = h (H-) - r \\] : \\(\\) density infected infectious humans; \\(H\\) density humans; \\(h\\) force infection (FoI), number infections, per perspon, per day; related daily entomological inoculation rate (dEIR). \\(r\\) clearance rate, number infections clear, per infected person, per day.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"parasite-infection-dynamics-in-mosquitoes-cal-yz","dir":"Articles","previous_headings":"The Modular Form","what":"Parasite Infection Dynamics in Mosquitoes, \\(\\cal YZ\\)","title":"Modular Forms for Disease Dynamics","text":"Similarly, equation describing infected mosquitoes following: \\[ dY/dt = \\kappa (M-Y) - g Y \\] : \\(Y\\) density infected mosquitoes; \\(M\\) density mosquitoes; \\(f\\) overall mosquito blood feeding rate, number human blood meals, per mosquito, per day; \\(q\\) human fraction; human blood feeding fraction blood feeding; \\(\\kappa\\) net infectiousness (NI) humans, probability mosquito become infected blood feeding human; related density infected humans. \\(g\\) mosquito death rate, number mosquitoes dying, per mosquito, per day;","code":""},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"blood-feeding","dir":"Articles","previous_headings":"The Modular Form","what":"Blood Feeding","title":"Modular Forms for Disease Dynamics","text":"two terms, FoI (\\(h\\)) NI (\\(\\kappa\\)), equations rely information comes equation. compute , need construct deal concept mixing, denote \\(\\beta\\). generic form, computation terms defines blood feeding model, interface \\(\\cal YZ\\) \\(\\cal X.\\)","code":""},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"force-of-infection-foi","dir":"Articles","previous_headings":"The Modular Form > Blood Feeding","what":"Force of Infection (FoI)","title":"Modular Forms for Disease Dynamics","text":"FoI \\(h\\) must related density infected mosquitoes. compute several steps. First, Ross-Macdonald model, density blood feeding mosquitoes given formula: \\[Z = F_Z(Y) = e^{-gn} Y\\] \\(n\\) extrinsic incubation period (EIP) Next, need compute EIR, computed distributing infective bites among humans. model, mixing uniform \\(\\beta = 1/H\\), write: \\[ E = \\beta \\cdot fqZ = \\frac {fqZ}H\\] finally, must compute FoI, draws information many different sources, \\[ h = F_h(E, ...) = b E.\\] \\(b\\) fraction infective bites cause infection;","code":""},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"net-infectiousness-ni","dir":"Articles","previous_headings":"The Modular Form > Blood Feeding","what":"Net Infectiousness (NI)","title":"Modular Forms for Disease Dynamics","text":"NI \\(\\kappa\\) must related density infected humans. Ross-Macdonald model, effective density infected humans : \\[X = F_X() = cI\\] \\(c\\) probability mosquito become infected blood feeding infected human. net infectiousness computed infective density averaged biting among humans. reasons become clear later, call \\(\\beta^T = 1/H\\): \\[\\kappa =  \\beta^T \\cdot X = \\frac XH\\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"computation","dir":"Articles","previous_headings":"","what":"Computation","title":"Modular Forms for Disease Dynamics","text":"solve equations, need write functions compute derivatives. using R package deSolve, derivative function constrained form: exDE, equations solved computing terms derivatives separately. Transmission(t,y,pars) computes three terms required compute parasite transmission blood feeding. stored main model object pars: pars$beta pars$EIR pars$NI Exposure(t, y, pars) computes FoI EIR model exposure stores pars$FoI instead developing models like RMv1, implemented code syle RMv2:","code":"RMv1 <- function(t, y, pars) {   with(pars,{       foi = b*exp(-g*n)*Y/H       kappa = c*I/H       dX = foi*(H-I) - r*I       dY = a*kappa*(M-Y) - g*Y        return(list(dX, dY))   }) } RMv2 <- function(t, y, pars) {   with(pars,{       pars = Transmission(t, y, pars)       pars = Exposure(t, y, pars)       dX = dXdt(t, y, pars)        dY = dMYZdt(t, y, pars)        return(list(dX, dY))   }) }"},{"path":"https://dd-harp.github.io/exDE/articles/modularity.html","id":"full-modularity","dir":"Articles","previous_headings":"","what":"Full Modularity","title":"Modular Forms for Disease Dynamics","text":"full structure computation exDE diagrammed Figure 2 easily examined corresponding code. One advantage modular notation possible set describe reasonably complex models fairly simple scripts. vignette 5-3-4 Example shows works. Figure 2","code":""},{"path":"https://dd-harp.github.io/exDE/articles/spat_metric.html","id":"human-movement","dir":"Articles","previous_headings":"","what":"Human Movement","title":"Spatial Metrics","text":"start fundamental matrix \\(\\Psi\\) dimension \\(p\\times n\\) , column \\(\\) gives distribution time risk strata places (rows). strata considered potentially risk 100% time, columns sum one, convention adopt document. \\(\\Psi_{ji}\\) fraction time strata \\(\\) spends patch \\(j\\).","code":""},{"path":"https://dd-harp.github.io/exDE/articles/spat_metric.html","id":"ambient-human-population","dir":"Articles","previous_headings":"","what":"Ambient Human Population","title":"Spatial Metrics","text":"Let \\(H\\) length \\(n\\) column vector giving population size strata. Let \\(w_{f}\\) length \\(n\\) column vector giving biting weights strata (null value \\(1\\)). want know \\(W\\), length \\(p\\) column vector tells us many people patch (summing strata ). \\[ W =\\begin{bmatrix} \\sum_{} \\Psi_{1i}w_{f1}H_{} \\\\ \\vdots \\\\ \\sum_{} \\Psi_{pi}w_{fi}H_{} \\end{bmatrix} = \\Psi \\cdot w_{f} H \\] element \\(W\\) gives total weighted person-time spent strata location.","code":""},{"path":"https://dd-harp.github.io/exDE/articles/spat_metric.html","id":"biting-distribution-matrix","dir":"Articles","previous_headings":"","what":"Biting Distribution Matrix","title":"Spatial Metrics","text":"biting distribution matrix \\(\\beta\\) \\(n \\times p\\) matrix central formulating mathematically consistent models bloodfeeding, , extension, consistent models mosquito-borne pathogen transmission. given mathematically : \\[ \\beta = \\mbox{diag}(w_{f}) \\cdot \\Psi^{\\top} \\cdot \\mbox{diag}(1/W) \\] can written component-wise : \\[ \\beta = \\begin{bmatrix} \\frac{\\Psi_{11}w_{f1}}{\\sum_{}\\Psi_{1i}w_{fi}H_{}} & \\cdots & \\frac{\\Psi_{p1}w_{f1}}{\\sum_{}\\Psi_{pi}w_{fi}H_{}} \\\\ \\vdots & & \\vdots \\\\ \\frac{\\Psi_{1n}w_{fn}}{\\sum_{}\\Psi_{1i}w_{fi}H_{}} & \\cdots & \\frac{\\Psi_{pn}w_{fn}}{\\sum_{}\\Psi_{pi}w_{fi}H_{}} \\end{bmatrix} \\] Now can get clearer impression \\(\\beta_{ij}\\) . probability bite mosquitoes patch \\(j\\) lands particular person strata \\(\\). Another way say proportion person-time spent single person strata \\(\\) patch \\(j\\), person-time spent patch. wanted look matrix whose columns sum unity elements give probability bite taken ambient population patch \\(j\\) land strata \\(\\), look following matrix: \\[ \\mbox{diag}(H) \\cdot \\beta \\] operation effect multiplying column \\(\\beta\\) diagonal matrix left, columns sum one (column sums \\(\\Psi\\), case total time risk \\(< 1\\)). Likewise want recover \\(\\Psi^{\\top}\\), \\(n \\times p\\) matrix whose rows describe strata distributes time across patches, one can simply multiply right \\(\\mbox{diag}(W)\\) effect multiplying column \\(\\beta\\) element diagonal \\(\\mbox{diag}(W)\\). \\[ \\beta \\cdot \\mbox{diag}(W) \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/spat_metric.html","id":"human-transmitting-capacity-htc","dir":"Articles","previous_headings":"","what":"Human transmitting capacity (HTC)","title":"Spatial Metrics","text":"Human transmitting capacity vector \\(D\\) length \\(n\\), element gives number net infectious days infected individual strata. homogeneous SIS model, simply: \\[ D = \\frac{c}{r} \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/spat_metric.html","id":"parasite-dispersal-by-mosquitoes","dir":"Articles","previous_headings":"","what":"Parasite dispersal by mosquitoes","title":"Spatial Metrics","text":"parasite dispersal mosquitoes matrix, \\(\\mathcal{V}\\) spatial analogue vectorial capacity, expected number humans infected per infected human, per day, assuming perfect transmission efficiency. \\[ \\mathcal{V} = fq\\Omega^{-1} \\cdot e^{-\\Omega\\tau} \\cdot \\mbox{diag}\\left(\\frac{fqM}{W}\\right) \\] can understood going right left. matrix \\(\\mbox{diag}\\left(\\frac{fqM}{W}\\right)\\) \\(p\\times p\\) matrix, diagonal giving numbers bloodmeals taken person patch, per day. Multiplying left \\(e^{-\\Omega\\tau}\\) effect multiplying column matrix left corresponding element diagonal matrix right. intermediate matrix columns describe bites/person patch distributed across patches extrinsic incubation period, accounting mortality period. final multiplication left distributes bites EIP passed. single patch, formula becomes: \\[ \\frac{fq}{g} e^{-g\\tau}fq\\frac{M}{H} \\] equivalent (substituting \\(H=W\\)) classic formula Smith McKenzie (2004): \\(\\frac{fq}{g}e^{-g\\tau}fq\\frac{M}{H}\\).","code":""},{"path":"https://dd-harp.github.io/exDE/articles/spat_metric.html","id":"parasite-dispersal-by-humans","dir":"Articles","previous_headings":"","what":"Parasite dispersal by humans","title":"Spatial Metrics","text":"\\[ \\mathcal{D} = \\mbox{diag}\\left(W \\right) \\cdot \\beta^T \\cdot \\mbox{diag}\\left(bDH\\right) \\cdot \\beta \\] can first examine multiplication \\(\\mbox{diag}\\left(bDH\\right) \\cdot \\beta\\) right. effect multiplying column \\(\\beta\\) diagonal \\(\\mbox{diag}\\left(bDH\\right)\\). results \\(n\\times p\\) matrix whose columns give distribution potentially transmitting person-time (\\(\\frac{bc}{r}\\)) person strata contributes patch. \\(p\\times p\\) matrix. left \\(\\mbox{diag}\\left(W \\right) \\cdot \\beta^T\\) multiplies column \\(\\beta^T\\) diagonal matrix; effect recovering original movement matrix \\(\\Psi\\). multiplying intermediate matrix produced preceding section left distributes potentially-transmitting person time across patches. Therefore \\(\\)-th column \\(\\mathcal{D}\\) describes potentially infectious person-time person infected \\(\\) distributed across patches. 1 patch, 1 strata case, simplifies considerably : \\[ \\mathcal{D} = \\frac{bc}{r} \\]","code":""},{"path":"https://dd-harp.github.io/exDE/articles/spat_metric.html","id":"parasite-dispersal-through-one-parasite-generation","dir":"Articles","previous_headings":"","what":"Parasite Dispersal through one Parasite Generation","title":"Spatial Metrics","text":"One way look parasite dispersal look parasites dispersed one parasite generation. can done mosquito mosquito, human human. show equation parasite dispersal generation, beginning ending human host. \\[ \\mathcal{R} =   b \\beta \\cdot {\\cal V}  \\cdot \\mbox{diag}\\left(W \\right) \\cdot \\beta^T  \\cdot \\mbox{diag}\\left(DH\\right) \\] \\(\\mathcal{R}\\) \\(n\\times n\\) matrix, columns describe infections starting strata disseminated among strata one generation. can learn interpret equation walking left right. \\(\\mbox{diag}\\left(W \\right) \\cdot \\beta^T \\cdot \\mbox{diag}\\left(DH\\right)\\) produces \\(p\\times n\\) matrix describes infectious person-time strata spread across patches. Multiplication \\(\\mathcal{V}\\) describes infectious person-time transformed potentially infectious bites mosquitoes, distributed space accounting mortality EIP. Final multiplication \\(\\beta\\) \\(b\\) takes account persons contact infectious bites, transmission efficiency back human hosts. , can take 1 patch, 1 strata case see formula simplifies: \\[ \\frac{bc}{r} \\cdot \\frac{fq}{g} e^{-g\\tau}fq\\frac{M}{H} \\] precisely formula \\(R_{0}\\) Smith McKenzie (2004). Therefore \\(\\mathcal{R}\\) “logical” spatial version threshold metric. track parasite dispersal mosquitoes mosquitoes arrive \\(p\\times p\\) matrix: \\[ \\mathcal{Z} = e^{-\\Omega\\tau} \\cdot \\mbox{diag}\\left( \\frac{fq M}{W} \\right) \\cdot {\\cal D} \\cdot  fq\\Omega^{-1} \\] 1 patch 1 strata case becomes equation \\(\\mathcal{R}\\).","code":""},{"path":"https://dd-harp.github.io/exDE/articles/spat_metric.html","id":"example","dir":"Articles","previous_headings":"","what":"Example","title":"Spatial Metrics","text":"demonstrate calculate metrics using 5-3-4 example. can visualize matrices heatmaps.","code":"library(exDE) library(ggplot2) l <- 5 p <- 3 n <- 4  calN <- matrix(   data = c(1,1,1,0,0,            0,0,0,1,1,            0,0,0,0,0),    nrow = p, ncol = l, byrow = TRUE )   xi <- matrix(c(.7, .2, .1, .8, .2), 5, 1)  calU <- t(calN %*% diag(as.vector(xi)))  g <- rep(1/12, p)  sigma <- rep(1/12/2, p)  calK <- t(matrix(   c(c(0, .6, .3),      c(.4, 0, .7),      c(.6, .4, 0)), 3, 3)) f <- rep(1/3, p)  q <- rep(0.9, p)  tau <- 12  M <- rep(100, p)  Omega <- diag(g) + (diag(1,p)-calK) %*% diag(sigma) Lambda <- Omega %*% M  H <- matrix(c(10,90, 100, 900), 4, 1) X <- as.vector(0.2*H) r <- rep(1/200, n) b <- rep(0.55, n) c <- c(0.1, .02, .1, .02)  calJ <- t(matrix(   c(c(0,0,0,0),     c(1,1,0,0),     c(0,0,1,1)), n, p ))  Theta <- t(matrix(   c(c(0.01,0.01,0.001,0.001),     c(.95,.92,.04,.02),     c(.04,.02,.959,.929)), n, p ))  W <- Theta %*% H beta <- t(Theta) %*% diag_inverse(W)  D <- c/r  calV <- metric_calV(f = f, q = q, Omega = Omega, tau = tau, M = M, W = W) calD <- metric_calD(W = W, beta = beta, b = b, D = D, H = H) calR <- metric_calR(b = b, beta = beta, calV = calV, W = W, D = D, H = H) calZ <- metric_calZ(Omega = Omega, tau = tau, f = f, q = q, M = M, W = W, calD = calD) calV_df <- data.frame(   value = as.vector(calV),   x = rep(1:nrow(calV), times = nrow(calV)),   y = rep(1:nrow(calV), each = nrow(calV)) )  ggplot(calV_df, aes(x=x,y=y,fill=log(value))) +     geom_raster() +     scale_y_reverse() +     guides(fill = 'none') +     theme(axis.title = element_blank())"},{"path":"https://dd-harp.github.io/exDE/articles/vc_lemenach.html","id":"parameters","dir":"Articles","previous_headings":"","what":"Parameters","title":"ITN-based Vector Control","text":"case study use simple model 3 patches, 3 population strata, 3 aquatic habitats. usual, set parameter values compute values state variables equilibrium. part equilibrium calculation must compute \\(\\Upsilon(0) = \\exp\\left(-\\int_{-\\tau}^{0} \\Omega(s) ds \\right)\\); value integrated mosquito demography matrix initial time point. simplify things, simply assume conditions constant prior \\(t=0\\) \\(\\Upsilon(0) = e^{-\\Omega\\tau}\\).","code":"nPatches <- 3 nVectors <- 1 nStrata <- 3 nHabitats <- 3  # human parameters b <- 0.55 c <- 0.15 r <- 1/200  wf <- rep(1, nStrata)  pfpr <- runif(n = nStrata, min = 0.25, max = 0.35) Hpop <- rpois(n = nStrata, lambda = 1000) X <- rbinom(n = nStrata, size = Hpop, prob = pfpr)  residence = c(1:3) searchWtsH = rep(1,3)   TaR <- matrix(   data = c(     0.9, 0.05, 0.05,     0.05, 0.9, 0.05,     0.05, 0.05, 0.9   ), nrow = nStrata, ncol = nPatches, byrow = T ) TaR <- t(TaR)  f <- 0.3  q <- 0.9  g <- 1/10  sigma <- 1/100  nu <- 1/2  eggsPerBatch <- 30 eip <- 11 calK = make_calK(nPatches, \"herethere\")"},{"path":"https://dd-harp.github.io/exDE/articles/vc_lemenach.html","id":"equilibrium","dir":"Articles","previous_headings":"","what":"Equilibrium","title":"ITN-based Vector Control","text":"Now compute equilibrium conditions adult mosquitoes human populations, PfPR human population maintained input levels conditions unchanging. Given equilibrium value \\(\\Lambda\\) required sustain mosquito populations level sufficient maintain transmission level PfPR, well values \\(\\psi\\) (maturation rate) \\(\\phi\\) (density independent mortality), compute equilibrium values \\(L\\) (aquatic mosquito density) \\(\\theta\\) (density dependent mortality).","code":"# derived EIR to sustain equilibrium pfpr EIR <- diag(1/b, nStrata) %*% ((r*X) / (Hpop - X))  # ambient pop W <- TaR %*% Hpop  # biting distribution matrix beta <- diag(wf) %*% t(TaR) %*% diag(1/as.vector(W), nPatches)  # kappa kappa <- t(beta) %*% (X*c)  Omega <- make_Omega(g = g, sigma = sigma, K = calK, nPatches = nPatches) Omega_inv <- solve(Omega) Upsilon <- expm::expm(-Omega * eip) Upsilon_inv <- expm::expm(Omega * eip)  # equilibrium solutions Z <- diag(1/(f*q), nPatches) %*% ginv(beta) %*% EIR MY <- diag(1/as.vector(f*q*kappa), nPatches) %*% Upsilon_inv %*% Omega %*% Z Y <- Omega_inv %*% (diag(as.vector(f*q*kappa), nPatches) %*% MY) M <- MY + Y P <- solve(diag(f, nPatches) + Omega) %*% diag(f, nPatches) %*% M Lambda <- Omega %*% M # aquatic habitat membership matrix (assume 1 habitat per patch) calN <- matrix(0, nPatches, nHabitats) diag(calN) <- 1  # egg dispersal matrix (assume 1 habitat per patch) calU <- matrix(0, nHabitats, nPatches) diag(calU) <- 1  psi <- 1/10 phi <- 1/12 eta <- as.vector(calU %*% (M * nu * eggsPerBatch))  alpha <- as.vector(solve(calN) %*% Lambda) L <- alpha/psi theta <- (eta - psi*L - phi*L)/(L^2)"},{"path":"https://dd-harp.github.io/exDE/articles/vc_lemenach.html","id":"setup","dir":"Articles","previous_headings":"","what":"Setup","title":"ITN-based Vector Control","text":"Now state variables solved equilibrium, can set parameters components system. use null model human demographic dynamics, assumes \\(H\\) constant time. ran model point, get baseline. Instead, set time-varying function compute coverage ITNs time point. use sine curve period 365 days goes 0 1 period, phase shifted 0 returns 0. function also returns 0 \\(t<0\\). must function takes single argument t (time) returns scalar value. use null model human demographic dynamics, assumes \\(H\\) constant time.","code":"# adult mosquito parameters Xo = list(b=b, c=c, r=r, X0=X)  Lo = list(psi=psi, phi=phi, theta=theta, L0=L)  MYZo = list(f=f, q=q, g=g, sigma=sigma,              nu=nu, eggsPerBatch=eggsPerBatch, eip=eip,              M0=M, P0=P, Y0=Y, Z0=Z) xde_setup(MYZname=\"RM\", Xname=\"SIS\", Lname=\"basic\",            nPatches=3, HPop=Hpop, membership=c(1:3), MYZopts=MYZo, calK=calK,            Xopts=Xo, residence=1:3, searchB=rep(1,3),            TimeSpent =TaR, searchQ=rep(1,3), Lopts=Lo) -> itn_mod itn_mod <- setup_control(itn_mod) # ITN coverage ITN_cov <- function(t) {ifelse(t < 0, 0, (sin(2*pi*(t-365/4) / 365) + 1) / 2)} itn_mod = setup_itn_lemenach(itn_mod, phi = ITN_cov) xde_solve(itn_mod, 5*365) -> itn_mod itn_mod$outputs$orbits$deout -> out"},{"path":"https://dd-harp.github.io/exDE/articles/vc_lemenach.html","id":"plot","dir":"Articles","previous_headings":"","what":"Plot","title":"ITN-based Vector Control","text":"can plot output study effects seasonal ITN coverage state variables. see total parous mosquito densities \\(M\\) \\(G\\) now vary sinusoidal manner coverage changes, \\(L\\), larval density, number ovipositing mosquitoes changes. addition increasing mosquito mortality, ITNs also decrease feeding rate proportion bloodmeals taken humans due repellency effect, see densities infected infectious mosquitoes (\\(Y\\) \\(Z\\)) steadily decrease time longer sufficient bloodmeals taken sustain prevalence. similar pattern appears human prevalence \\(X\\), slower dynamics due slow recovery rate untreated infection.","code":"colnames(out)[itn_mod$ix$L[[1]]$L_ix+1] <- paste0('L_', 1:itn_mod$nHabitats) colnames(out)[itn_mod$ix$MYZ[[1]]$M_ix+1] <- paste0('M_', 1:itn_mod$nPatches) colnames(out)[itn_mod$ix$MYZ[[1]]$P_ix+1] <- paste0('P_', 1:itn_mod$nPatches) colnames(out)[itn_mod$ix$MYZ[[1]]$Y_ix+1] <- paste0('Y_', 1:itn_mod$nPatches) colnames(out)[itn_mod$ix$MYZ[[1]]$Z_ix+1] <- paste0('Z_', 1:itn_mod$nPatches) colnames(out)[itn_mod$ix$X[[1]]$X_ix+1] <- paste0('X_', 1:itn_mod$Hpar[[1]]$nStrata)  out <- out[, -c(itn_mod$ix$MYZ[[1]]$sigma_ix+1)] out <- out[, -c(itn_mod$ix$MYZ[[1]]$g_ix+1)] out <- out[, -c(itn_mod$ix$MYZ[[1]]$fqkappa_ix+1)] out <- out[, -c(itn_mod$ix$MYZ[[1]]$Upsilon_ix+1)]  out <- as.data.table(out) out <- melt(out, id.vars = 'time') out[, c(\"Component\", \"Stratification\") := tstrsplit(variable, '_', fixed = TRUE)] out[, variable := NULL]  ggplot(data = out, mapping = aes(x = time, y = value, color = Stratification)) +   geom_line() +   facet_wrap(. ~ Component, scales = 'free') +   theme_bw()"},{"path":"https://dd-harp.github.io/exDE/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Sean L. Wu. Author, maintainer. David L. Smith. Author.","code":""},{"path":"https://dd-harp.github.io/exDE/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Wu S, Henry J, Citron D, Ssebuliba D, Nsumba J, Sánchez C. H, Brady O, Guerra C, García G, Carter , Ferguson H, Afolabi B, Hay S, Reiner R, Kiware S, Smith D (2022). “Spatial Dynamics Malaria Transmission.” medRxiv. doi:10.1101/2022.11.07.22282044, https://www.medrxiv.org/content/10.1101/2022.11.07.22282044v1.","code":"@Article{,   title = {Spatial Dynamics of Malaria Transmission},   author = {Sean L. Wu and John M. Henry and Daniel T. Citron and Doreen M. Ssebuliba and Juliet N. Nsumba and Héctor M. {Sánchez C.} and Oliver J. Brady and Carlos A. Guerra and Guillermo A. García and Austin R. Carter and Heather M. Ferguson and Bakare E. Afolabi and Simon I. Hay and Robert C. Reiner and Samson Kiware and David L. Smith},   journal = {medRxiv},   year = {2022},   publisher = {Cold Spring Harbor Laboratory Press},   url = {https://www.medrxiv.org/content/10.1101/2022.11.07.22282044v1},   doi = {10.1101/2022.11.07.22282044}, }"},{"path":[]},{"path":"https://dd-harp.github.io/exDE/index.html","id":"what-is-exde","dir":"","previous_headings":"","what":"What is exDE?","title":"Extensible Differential Equations for Mosquito-Borne Pathogen Modeling","text":"exDE software implements mathematical framework setting , analyzing, solving models mosquito-borne pathogen dynamics control systems ordinary delay differential equations. framework designed model spatial transmission dynamics pathogen within defined spatial domain; spatial ecology population dynamics mosquitoes within domain; exogenous forcing weather vector control; malaria mosquito importation. software also supports population dynamic models stratified human populations, including aging demographic changes. main focus software development malaria, framework capabilities model mosquito-transmitted pathogens. software aims fully modular: implements plug--play computation broad class simulation models describing dynamics control mosquito-transmitted pathogens. Modularity achieved combination methods: functions compute derivatives use method dispatches parameter lists component used compute full set differential equations; interfaces blood feeding egg laying biologically realistic rigidly defined guarantee mathematical consistency; large set additional features implemented careful attention detail guarantee consistency avoid conflicts. function exDE::xDE_diffeqn computes gradient state variables modular components can used excellent solvers deSolve, differential equation solvers R. exDE can regarded continuous-time companion discrete stochastic Micro-MoB framework. get started, please consider reading articles drop panels , website. 3 sections ending “Component” describe particular models implementing interface components (adult mosquitoes, aquatic mosquitoes, humans), show simulation equilibrium values. section “Articles” -depth examples, including extended walk set run model vignette(\"ex_534\"), guide contribute, example running model exDE external forcing model ITN (insecticide treated nets) based vector control vignette(\"vc_lemenach\"). section “Functions” documents function exported package.","code":""},{"path":"https://dd-harp.github.io/exDE/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Extensible Differential Equations for Mosquito-Borne Pathogen Modeling","text":"install latest version GitHub, run following lines code R session. Alternatively, can install directly CRAN (please aware version CRAN may latest version GitHub):","code":"library(devtools) devtools::install_github(\"dd-harp/exDE\") install.packages(\"exDE\")"},{"path":"https://dd-harp.github.io/exDE/index.html","id":"contributing","dir":"","previous_headings":"","what":"Contributing","title":"Extensible Differential Equations for Mosquito-Borne Pathogen Modeling","text":"information contribute development exDE, please read article contribute vignette(\"Contributing\")! questions, comments, bug reports, suggestions, first point contact development team GitHub Issues. specifically submitting bug report, please check bug reporting guide. interested collaborating extensive model development (e.g. new mosquito model), please hesitate contact authors, whose email addresses can found DESCRIPTION file. welcome issues encourage contribution regardless experience; length contributing guide intended intimidating, merely complete. responsibility package maintainers help new contributors understand conventions guide contributions successful conclusion.","code":""},{"path":"https://dd-harp.github.io/exDE/index.html","id":"model-building-in-exde","dir":"","previous_headings":"","what":"Model building in exDE","title":"Extensible Differential Equations for Mosquito-Borne Pathogen Modeling","text":"Models mosquito borne pathogen transmission systems naturally modular, structured vector life stage, host population strata, spatial locations (patches) transmission occurs (see figure ).  Models exDE framework constructed 3 dynamical components: ℳ: adult mosquitoes, whose dynamics described dℳ/dt ℒ: aquatic (immature) mosquitoes, whose dynamics described dℒ/dt 𝒳: human population, whose dynamics described d𝒳/dt combined state 3 components entire state dynamical model, combined dynamics described differential equations represents full endogenous dynamics system. addition 2 components directly contribute state model, instead modify parameters compute intermediate quantities represent external influences system. : Exogenous forcing: weather, climate, unmodeled populations Vector control: public health mosquito control interventions affect dynamical components also functions handle exchange information (flows) dynamical components couple dynamics. Bloodfeeding process adult mosquitoes seek feed blood hosts, results quantities EIR (entomological inoculation rate) κ, net infectiousness humans mosquitoes, couple dynamics ℳ 𝒳. Likewise emergence new adults aquatic habitats egg laying adults habitats couples ℳ ℒ. function exDE::xDE_diffeqn compute necessary quantities returns vector derivatives state variables can used solve trajectories model exDE. program flow within function summarized diagram:  information, please read research article describing theory behind model.","code":""},{"path":"https://dd-harp.github.io/exDE/index.html","id":"acknowledgements","dir":"","previous_headings":"","what":"Acknowledgements","title":"Extensible Differential Equations for Mosquito-Borne Pathogen Modeling","text":"Version 1.0 software designed Sean L. Wu Professor David L. Smith. code written Sean L. Wu. anticipate active development exDE MicroMoB add new models fill important needs. idea developing modular software simulate dynamics control mosquito-borne pathogens originated sometime around 2009 Emerging Pathogens Institute, University Florida. took much longer anticipated finish. concepts appeared various publications. algorithms trace back software packages never launched, someday might yet completed (e.g., MASH). retrospect, key challenge blood feeding, one. inception, project supported grants Bill Melinda Gates Foundation, including (recently) Modeling Adaptive Malaria Control (INV 030600, PI = David L Smith, University Washington). software part RAMP (Robust Analytics Malaria Policy), core analytical methodology developed support adaptive malaria control. RAMP project includes RAMP-UW team University Washington based Seattle Washington, RAMP-Uganda team based Kampala, Uganda, provides analytics support National Malaria Control Division, Ministry Health, Uganda. model features inspired discussions mosquito working groups (led Professor Thomas Scott) RAPIDD (Research Policy Infectious Disease Dynamics). time, project benefited unwavering support inspiration late F. Ellis McKenzie, Fogarty International Center. Development exDE supported, part, grant US National Institute Allergies Infectious Diseases (NIAID) fund project Spatial Targeting Adaptive Vector Control Residual Transmission Malaria Elimination Urban African Settings (R01 AI163398, PI = David L Smith), supported collaboration Bioko Island Malaria Elimination Program. Development software benefited funding collaboration NIAID grant Program Resistance, Immunology, Surveillance & Modeling Malaria Uganda (PRISM) (2U19AI089674, PIs = Grant Dorsey, University California San Francisco; Moses Kamya, Infectious Diseases Research Collaboration), part International Centers Excellence Malaria Research (ICEMR) program. Funding develop models West Nile Virus support Harris County Public Health funded NSF part project, Computing Biome (PI= Janos Sztipanovits). project part Convergence Accelerator program National Science Foundation, Directorate Technology, Innovation, Partnerships (TIP) (NSF 2040688 NSF 2040688, PI=Janos Sztipanovits, Vanderbilt University).","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up exogenous variables for abiotic forcing — Abiotic.forced","title":"Set up exogenous variables for abiotic forcing — Abiotic.forced","text":"Implements Abiotic abiotic forcing","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up exogenous variables for abiotic forcing — Abiotic.forced","text":"","code":"# S3 method for forced Abiotic(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up exogenous variables for abiotic forcing — Abiotic.forced","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up exogenous variables for abiotic forcing — Abiotic.forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up exogenous variables for abiotic forcing — Abiotic","title":"Set up exogenous variables for abiotic forcing — Abiotic","text":"method dispatches type pars$ABIOTIC.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up exogenous 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(nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up exogenous variables for abiotic forcing — Abiotic.null","text":"","code":"# S3 method for null Abiotic(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up exogenous variables for abiotic forcing — Abiotic.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Abiotic.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up exogenous variables for abiotic forcing — Abiotic.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSpray.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for mass spraying — AreaSpray","title":"Methods for mass 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AreaSpray null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSpray.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up mass spraying — AreaSpray.null","text":"","code":"# S3 method for null AreaSpray(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AreaSpray.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up mass spraying — AreaSpray.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSpray.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up mass spraying — AreaSpray.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffectSizes.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for mass spraying — AreaSprayEffectSizes","title":"Methods for mass spraying — AreaSprayEffectSizes","text":"method dispatches type pars$AREA_SPRAY.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffectSizes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for mass spraying — AreaSprayEffectSizes","text":"","code":"AreaSprayEffectSizes(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffectSizes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for mass spraying — AreaSprayEffectSizes","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffectSizes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for mass spraying — AreaSprayEffectSizes","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffectSizes.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up mass spraying — AreaSprayEffectSizes.null","title":"Set up mass spraying — AreaSprayEffectSizes.null","text":"Implements AreaSprayEffectSizes null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffectSizes.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up mass spraying — AreaSprayEffectSizes.null","text":"","code":"# S3 method for null AreaSprayEffectSizes(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffectSizes.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up mass spraying — AreaSprayEffectSizes.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffectSizes.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up mass spraying — AreaSprayEffectSizes.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffects.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for mass spraying — AreaSprayEffects","title":"Methods for mass spraying — AreaSprayEffects","text":"method dispatches type pars$AREA_SPRAY.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for mass spraying — AreaSprayEffects","text":"","code":"AreaSprayEffects(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for mass spraying — AreaSprayEffects","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for mass spraying — AreaSprayEffects","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffects.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up mass spraying — AreaSprayEffects.null","title":"Set up mass spraying — AreaSprayEffects.null","text":"Implements AreaSprayEffects null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffects.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up mass spraying — AreaSprayEffects.null","text":"","code":"# S3 method for null AreaSprayEffects(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffects.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up mass spraying — AreaSprayEffects.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AreaSprayEffects.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up mass spraying — AreaSprayEffects.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute availability of local humans for blood feeding — AvailableBlood.forced","title":"Compute availability of local humans for blood feeding — AvailableBlood.forced","text":"Compute availability pathogen's hosts blood feeding","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute availability of local humans for blood feeding — AvailableBlood.forced","text":"","code":"# S3 method for forced AvailableBlood(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute availability of local humans for blood feeding — AvailableBlood.forced","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute availability of local humans for blood feeding — AvailableBlood.forced","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.html","id":null,"dir":"Reference","previous_headings":"","what":"Update the availability of blood hosts — AvailableBlood","title":"Update the availability of blood hosts — AvailableBlood","text":"method dispatches type pars$BFpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update the availability of blood hosts — AvailableBlood","text":"","code":"AvailableBlood(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update the availability of blood hosts — AvailableBlood","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update the availability of blood hosts — AvailableBlood","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.setup.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute availability of local humans for blood feeding — AvailableBlood.setup","title":"Compute availability of local humans for blood feeding — AvailableBlood.setup","text":"Compute availability pathogen's hosts blood feeding","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.setup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute availability of local humans for blood feeding — AvailableBlood.setup","text":"","code":"# S3 method for setup AvailableBlood(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.setup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute availability of local humans for blood feeding — AvailableBlood.setup","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.setup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute availability of local humans for blood feeding — AvailableBlood.setup","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute availability of local humans for blood feeding — AvailableBlood.static","title":"Compute availability of local humans for blood feeding — AvailableBlood.static","text":"Compute availability pathogen's hosts blood feeding","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute availability of local humans for blood feeding — AvailableBlood.static","text":"","code":"# S3 method for static AvailableBlood(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute availability of local humans for blood feeding — AvailableBlood.static","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableBlood.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute availability of local humans for blood feeding — AvailableBlood.static","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute total availability of aquatic habitats — AvailableHabitat.forced","title":"Compute total availability of aquatic habitats — AvailableHabitat.forced","text":"Computes availability aquatic habitats","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute total availability of aquatic habitats — AvailableHabitat.forced","text":"","code":"# S3 method for forced AvailableHabitat(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute total availability of aquatic habitats — AvailableHabitat.forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute total availability of aquatic habitats — AvailableHabitat.forced","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.html","id":null,"dir":"Reference","previous_headings":"","what":"Update the availability of aquatic habitats — AvailableHabitat","title":"Update the availability of aquatic habitats — AvailableHabitat","text":"method dispatches type pars$EGGpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update the availability of aquatic habitats — AvailableHabitat","text":"","code":"AvailableHabitat(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update the availability of aquatic habitats — AvailableHabitat","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update the availability of aquatic habitats — AvailableHabitat","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.simple.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute total availability of aquatic habitats — AvailableHabitat.simple","title":"Compute total availability of aquatic habitats — AvailableHabitat.simple","text":"Computes availability aquatic habitats static model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.simple.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute total availability of aquatic habitats — AvailableHabitat.simple","text":"","code":"# S3 method for simple AvailableHabitat(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.simple.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute total availability of aquatic habitats — AvailableHabitat.simple","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.simple.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute total availability of aquatic habitats — AvailableHabitat.simple","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute total availability of aquatic habitats — AvailableHabitat.static","title":"Compute total availability of aquatic habitats — AvailableHabitat.static","text":"Computes availability aquatic habitats static model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute total availability of aquatic habitats — AvailableHabitat.static","text":"","code":"# S3 method for static AvailableHabitat(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute total availability of aquatic habitats — AvailableHabitat.static","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableHabitat.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute total availability of aquatic habitats — AvailableHabitat.static","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute total availability of sugar — AvailableSugar.forced","title":"Compute total availability of sugar — AvailableSugar.forced","text":"Computes availability sugar","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute total availability of sugar — AvailableSugar.forced","text":"","code":"# S3 method for forced 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pars$SUGAR.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update the availability of sugar — AvailableSugar","text":"","code":"AvailableSugar(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update the availability of sugar — AvailableSugar","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update the availability of sugar — AvailableSugar","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/AvailableSugar.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute total availability of sugar — AvailableSugar.static","title":"Compute total availability of sugar — 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nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify baseline bionomic parameters, called from VectorControlEffectSizes — BedNetEffectSizes","title":"Modify baseline bionomic parameters, called from VectorControlEffectSizes — BedNetEffectSizes","text":"method dispatches type pars$ITNefsz.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify baseline bionomic parameters, called from VectorControlEffectSizes — BedNetEffectSizes","text":"","code":"BedNetEffectSizes(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify baseline bionomic parameters, called from VectorControlEffectSizes — BedNetEffectSizes","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify baseline bionomic parameters, called from VectorControlEffectSizes — BedNetEffectSizes","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.lemenach.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify baseline values due to vector control — BedNetEffectSizes.lemenach","title":"Modify baseline values due to vector control — BedNetEffectSizes.lemenach","text":"Implements BedNetEffectSizes Le Menach ITN model vector control","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.lemenach.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify baseline values due to vector control — BedNetEffectSizes.lemenach","text":"","code":"# S3 method for lemenach BedNetEffectSizes(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.lemenach.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify baseline values due to vector control — BedNetEffectSizes.lemenach","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.lemenach.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify baseline values due to vector control — BedNetEffectSizes.lemenach","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Bed net ownership — BedNetEffectSizes.null","title":"Bed net ownership — BedNetEffectSizes.null","text":"Implements BedNetEffectSizes null model bed nets (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bed net ownership — BedNetEffectSizes.null","text":"","code":"# S3 method for null BedNetEffectSizes(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bed net ownership — BedNetEffectSizes.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffectSizes.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bed net ownership — BedNetEffectSizes.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffects.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify variables or parameters, called from VectorControlEffects — BedNetEffects","title":"Modify variables or parameters, called from VectorControlEffects — BedNetEffects","text":"method dispatches type pars$ITNeff.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify variables or parameters, called from VectorControlEffects — BedNetEffects","text":"","code":"BedNetEffects(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify variables or parameters, called from VectorControlEffects — BedNetEffects","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify variables or parameters, called from VectorControlEffects — BedNetEffects","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffects.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Bed net ownership — BedNetEffects.null","title":"Bed net ownership — BedNetEffects.null","text":"Implements BedNetEffects null model bed nets (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffects.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bed net ownership — BedNetEffects.null","text":"","code":"# S3 method for null BedNetEffects(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffects.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bed net ownership — BedNetEffects.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/BedNetEffects.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bed net ownership — BedNetEffects.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for dynamic human and mosquito behaviors — Behavior.forced","title":"Methods for dynamic human and mosquito behaviors — Behavior.forced","text":"Implements Behavior forced model (changes)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for dynamic human and mosquito behaviors — Behavior.forced","text":"","code":"# S3 method for forced Behavior(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for dynamic human and mosquito behaviors — Behavior.forced","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for dynamic human and mosquito behaviors — Behavior.forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for dynamic human and mosquito behaviors — Behavior","title":"Methods for dynamic human and mosquito behaviors — Behavior","text":"method dispatches type pars$BEHAVIOR.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for dynamic human and mosquito behaviors — Behavior","text":"","code":"Behavior(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for dynamic human and mosquito behaviors — Behavior","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for dynamic human and mosquito behaviors — Behavior","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for dynamic human and mosquito behaviors — Behavior.null","title":"Methods for dynamic human and mosquito behaviors — Behavior.null","text":"Implements Behavior null model (changes)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for dynamic human and mosquito behaviors — Behavior.null","text":"","code":"# S3 method for null Behavior(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for dynamic human and mosquito behaviors — Behavior.null","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Behavior.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for dynamic human and mosquito behaviors — Behavior.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.Ldynamic.html","id":null,"dir":"Reference","previous_headings":"","what":"Set bionomic parameter rates relative to baseline — Bionomics.Ldynamic","title":"Set bionomic parameter rates relative to baseline — Bionomics.Ldynamic","text":"calls Lbionomics species time step","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.Ldynamic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set bionomic parameter rates relative to baseline — Bionomics.Ldynamic","text":"","code":"# S3 method for Ldynamic Bionomics(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.Ldynamic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set bionomic parameter rates relative to baseline — Bionomics.Ldynamic","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.Ldynamic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set bionomic parameter rates relative to baseline — Bionomics.Ldynamic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.Mdynamic.html","id":null,"dir":"Reference","previous_headings":"","what":"Set bionomic parameter rates relative to baseline — Bionomics.Mdynamic","title":"Set bionomic parameter rates relative to baseline — Bionomics.Mdynamic","text":"calls Mbionomics Lbionmics species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.Mdynamic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set bionomic parameter rates relative to baseline — Bionomics.Mdynamic","text":"","code":"# S3 method for Mdynamic Bionomics(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.Mdynamic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set bionomic parameter rates relative to baseline — Bionomics.Mdynamic","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.Mdynamic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set bionomic parameter rates relative to baseline — Bionomics.Mdynamic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.dynamic.html","id":null,"dir":"Reference","previous_headings":"","what":"Set bionomic parameter rates relative to baseline — Bionomics.dynamic","title":"Set bionomic parameter rates relative to baseline — Bionomics.dynamic","text":"calls Mbionomics Lbionmics species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.dynamic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set bionomic parameter rates relative to baseline — Bionomics.dynamic","text":"","code":"# S3 method for dynamic Bionomics(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.dynamic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set bionomic parameter rates relative to baseline — Bionomics.dynamic","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.dynamic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set bionomic parameter rates relative to baseline — Bionomics.dynamic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.html","id":null,"dir":"Reference","previous_headings":"","what":"Set bionomic parameter rates relative to baseline — Bionomics","title":"Set bionomic parameter rates relative to baseline — Bionomics","text":"calls Mbionomics Lbionmics species. function resets bionomic parameters pre-control baseline value, can later modified vector control. models, pre-control baseline computed function resource availability.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set bionomic parameter rates relative to baseline — Bionomics","text":"","code":"Bionomics(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set bionomic parameter rates relative to baseline — Bionomics","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set bionomic parameter rates relative to baseline — Bionomics","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.setup.html","id":null,"dir":"Reference","previous_headings":"","what":"Set bionomic parameter rates relative to baseline — Bionomics.setup","title":"Set bionomic parameter rates relative to baseline — Bionomics.setup","text":"calls Mbionomics Lbionmics species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.setup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set bionomic parameter rates relative to baseline — Bionomics.setup","text":"","code":"# S3 method for setup Bionomics(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.setup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set bionomic parameter rates relative to baseline — Bionomics.setup","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.setup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set bionomic parameter rates relative to baseline — Bionomics.setup","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Set bionomic parameter rates relative to baseline — Bionomics.static","title":"Set bionomic parameter rates relative to baseline — Bionomics.static","text":"calls Mbionomics Lbionmics species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set bionomic parameter rates relative to baseline — Bionomics.static","text":"","code":"# S3 method for static Bionomics(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set bionomic parameter rates relative to baseline — Bionomics.static","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Bionomics.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set bionomic parameter rates relative to baseline — Bionomics.static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Births.html","id":null,"dir":"Reference","previous_headings":"","what":"A function that computes the birth rate for human populations — Births","title":"A function that computes the birth rate for human populations — Births","text":"method dispatches type pars$Hpar$Births","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Births.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function that computes the birth rate for human populations — Births","text":"","code":"Births(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/Births.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function that computes the birth rate for human populations — Births","text":"t current simulation time y state vector pars list index host species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Births.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function that computes the birth rate for human populations — Births","text":"see help pages specific methods","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Births.zero.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives of demographic changes in human populations — Births.zero","title":"Derivatives of demographic changes in human populations — Births.zero","text":"Implements Births static population models","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Births.zero.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives of demographic changes in human populations — Births.zero","text":"","code":"# S3 method for zero Births(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/Births.zero.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives of demographic changes in human populations — Births.zero","text":"t current simulation time y state vector pars list index host species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Births.zero.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives of demographic changes in human populations — Births.zero","text":"numeric vector zeros","code":""},{"path":"https://dd-harp.github.io/exDE/reference/CareSeeking.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of exogenous variables describing care seeking — CareSeeking","title":"Set the values of exogenous variables describing care seeking — CareSeeking","text":"method dispatches type pars$CARE_SEEKING.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/CareSeeking.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of exogenous variables describing care seeking — CareSeeking","text":"","code":"CareSeeking(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/CareSeeking.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of exogenous variables describing care seeking — CareSeeking","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/CareSeeking.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of exogenous variables describing care seeking — CareSeeking","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/CareSeeking.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of exogenous variables describing care seeking — CareSeeking.null","title":"Set the values of exogenous variables describing care seeking — CareSeeking.null","text":"Implements CareSeeking null model care seeking (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/CareSeeking.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of exogenous variables describing care seeking — CareSeeking.null","text":"","code":"# S3 method for null CareSeeking(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/CareSeeking.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of exogenous variables describing care seeking — CareSeeking.null","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/CareSeeking.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of exogenous variables describing care seeking — CareSeeking.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up exogenous variables for civil forcing — Civil.forced","title":"Set up exogenous variables for civil forcing — Civil.forced","text":"Implements Civil civil forcing","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up exogenous variables for civil forcing — Civil.forced","text":"","code":"# S3 method for forced Civil(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Civil.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up exogenous variables for civil forcing — Civil.forced","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up exogenous variables for civil forcing — Civil.forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up exogenous variables for civil forcing — Civil","title":"Set up exogenous variables for civil forcing — Civil","text":"method dispatches type pars$CIVIL.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up exogenous variables for civil forcing — Civil","text":"","code":"Civil(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Civil.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up exogenous variables for civil forcing — Civil","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up exogenous variables for civil forcing — Civil","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up exogenous variables for civil forcing — Civil.null","title":"Set up exogenous variables for civil forcing — Civil.null","text":"Implements Civil null model exogenous forcing (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up exogenous variables for civil forcing — Civil.null","text":"","code":"# S3 method for null Civil(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Civil.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up exogenous variables for civil forcing — Civil.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Civil.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up exogenous variables for civil forcing — Civil.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Clinic.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for distributing interventions during clinical visits — Clinic","title":"Methods for distributing interventions during clinical visits — Clinic","text":"method dispatches type pars$CLINIC.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Clinic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for distributing interventions during clinical visits — Clinic","text":"","code":"Clinic(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Clinic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for distributing interventions during clinical visits — Clinic","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Clinic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for distributing interventions during clinical visits — Clinic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Clinic.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for distributing interventions during clinical visits — Clinic.null","title":"Methods for distributing interventions during clinical visits — Clinic.null","text":"Implements Clinic null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Clinic.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for distributing interventions during clinical visits — Clinic.null","text":"","code":"# S3 method for null Clinic(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Clinic.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for distributing interventions during clinical visits — Clinic.null","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Clinic.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for distributing interventions during clinical visits — Clinic.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify parameters due to exogenous forcing by all kinds of control — Control.forced","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.forced","text":"Implements Control model control","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.forced","text":"","code":"# S3 method for forced Control(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Control.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.forced","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify parameters due to exogenous forcing by all kinds of control — Control","title":"Modify parameters due to exogenous forcing by all kinds of control — Control","text":"method dispatches type pars$CONTROL.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify parameters due to exogenous forcing by all kinds of control — Control","text":"","code":"Control(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify parameters due to exogenous forcing by all kinds of control — Control","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify parameters due to exogenous forcing by all kinds of control — Control","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify parameters due to exogenous forcing by all kinds of control — Control.null","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.null","text":"Implements Control null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.null","text":"","code":"# S3 method for null Control(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Control.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.null","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify parameters due to exogenous forcing by all kinds of control — Control.static","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.static","text":"Implements Control static model; setting , nothing","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.static","text":"","code":"# S3 method for static Control(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Control.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.static","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Control.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify parameters due to exogenous forcing by all kinds of control — Control.static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Development.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up developments — Development","title":"Set up developments — Development","text":"method dispatches type pars$DEVELOPMENT.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Development.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up developments — Development","text":"","code":"Development(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Development.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up developments — Development","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Development.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up developments — Development","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Development.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up developments — Development.null","title":"Set up developments — Development.null","text":"Implements Development null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Development.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up developments — Development.null","text":"","code":"# S3 method for null Development(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Development.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up developments — Development.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Development.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up developments — Development.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/DistributeBedNets.html","id":null,"dir":"Reference","previous_headings":"","what":"Distribute bed nets, called from Control(VectorControl) — DistributeBedNets","title":"Distribute bed nets, called from Control(VectorControl) — DistributeBedNets","text":"method dispatches type pars$ITNdist.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/DistributeBedNets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Distribute bed nets, called from Control(VectorControl) — DistributeBedNets","text":"","code":"DistributeBedNets(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/DistributeBedNets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Distribute bed nets, called from Control(VectorControl) — DistributeBedNets","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/DistributeBedNets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Distribute bed nets, called from Control(VectorControl) — DistributeBedNets","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/DistributeBedNets.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Distribute bed nets — DistributeBedNets.null","title":"Distribute bed nets — DistributeBedNets.null","text":"Implements DistributeBedNets null model bed nets (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/DistributeBedNets.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Distribute bed nets — DistributeBedNets.null","text":"","code":"# S3 method for null DistributeBedNets(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/DistributeBedNets.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Distribute bed nets — DistributeBedNets.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/DistributeBedNets.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Distribute bed nets — DistributeBedNets.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the EIP — EIP","title":"Compute the EIP — EIP","text":"method dispatches type EIPmod.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the EIP — EIP","text":"","code":"EIP(t, EIPmod)"},{"path":"https://dd-harp.github.io/exDE/reference/EIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the EIP — EIP","text":"t current simulation time EIPmod list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the EIP — EIP","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EIP.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify parameters due to exogenous forcing by all kinds of control — EIP.static","title":"Modify parameters due to exogenous forcing by all kinds of control — EIP.static","text":"Implements EIP static model (EIP constant)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EIP.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify parameters due to exogenous forcing by all kinds of control — EIP.static","text":"","code":"# S3 method for static EIP(t, EIPmod)"},{"path":"https://dd-harp.github.io/exDE/reference/EIP.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify parameters due to exogenous forcing by all kinds of control — EIP.static","text":"t current simulation time EIPmod list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EIP.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify parameters due to exogenous forcing by all kinds of control — EIP.static","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.dynamic.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute eggs laid — EggLaying.dynamic","title":"Compute eggs laid — EggLaying.dynamic","text":"Computes eggs laid s^th species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.dynamic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute eggs laid — EggLaying.dynamic","text":"","code":"# S3 method for dynamic EggLaying(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.dynamic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute eggs laid — EggLaying.dynamic","text":"t time y state variables pars model object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.dynamic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute eggs laid — EggLaying.dynamic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute eggs laid — EggLaying","title":"Compute eggs laid — EggLaying","text":"Computes eggs laid s^th species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute eggs laid — EggLaying","text":"","code":"EggLaying(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute eggs laid — EggLaying","text":"t time y state variables pars model object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute eggs laid — EggLaying","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.setup.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute eggs laid — EggLaying.setup","title":"Compute eggs laid — EggLaying.setup","text":"Computes eggs laid s^th species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.setup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute eggs laid — EggLaying.setup","text":"","code":"# S3 method for setup EggLaying(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.setup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute eggs laid — EggLaying.setup","text":"t time y state variables pars model object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.setup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute eggs laid — EggLaying.setup","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.simple.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute eggs laid — EggLaying.simple","title":"Compute eggs laid — EggLaying.simple","text":"Computes eggs laid s^th species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.simple.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute eggs laid — EggLaying.simple","text":"","code":"# S3 method for simple EggLaying(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.simple.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute eggs laid — EggLaying.simple","text":"t time y state variables pars model object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.simple.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute eggs laid — EggLaying.simple","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute eggs laid — EggLaying.static","title":"Compute eggs laid — EggLaying.static","text":"Computes eggs laid s^th species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute eggs laid — EggLaying.static","text":"","code":"# S3 method for static EggLaying(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute eggs laid — EggLaying.static","text":"t time y state variables pars model object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/EggLaying.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute eggs laid — EggLaying.static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Emergence.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute emerging adults — Emergence","title":"Compute emerging adults — Emergence","text":"Computes eggs laid s^th species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Emergence.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute emerging adults — Emergence","text":"","code":"Emergence(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Emergence.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute emerging adults — Emergence","text":"t time y state variables pars model object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Emergence.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute emerging adults — Emergence","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Exposure.html","id":null,"dir":"Reference","previous_headings":"","what":"Exposure and Infection — Exposure","title":"Exposure and Infection — Exposure","text":"function translates local daily entomological inoculation rate (dEIR), computed one transmission terms measure daily force infection (dFoI). daily FoI sum two terms: 1) function F_foi computes local dFoI; 2) function travel_malaria computes FoI resulting exposure traveling.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Exposure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Exposure and Infection — Exposure","text":"","code":"Exposure(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Exposure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Exposure and Infection — Exposure","text":"t time y state variables pars model object list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Exposure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Exposure and Infection — Exposure","text":"function modifies pars returns : computed FoI stored pars$FoI","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_EIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Entomological inoculation rate on human strata — F_EIR","title":"Entomological inoculation rate on human strata — F_EIR","text":"Compute daily EIR strata time t","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_EIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Entomological inoculation rate on human strata — F_EIR","text":"","code":"F_EIR(t, y, pars, i, s)"},{"path":"https://dd-harp.github.io/exDE/reference/F_EIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Entomological inoculation rate on human strata — F_EIR","text":"t current simulation time y state vector pars list host species index s vector species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_EIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Entomological inoculation rate on human strata — F_EIR","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_H.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of effective infectious human population — F_H.SIP","title":"Size of effective infectious human population — F_H.SIP","text":"Implements F_X SIP model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_H.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of effective infectious human population — F_H.SIP","text":"","code":"# S3 method for SIP F_H(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/F_H.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of effective infectious human population — F_H.SIP","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_H.SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Size of effective infectious human population — F_H.SIP","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_H.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of effective infectious human population — F_H.SIS","title":"Size of effective infectious human population — F_H.SIS","text":"Implements F_H SIS model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_H.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of effective infectious human population — F_H.SIS","text":"","code":"# S3 method for SIS F_H(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/F_H.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of effective infectious human population — F_H.SIS","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_H.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Size of effective infectious human population — F_H.SIS","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_H.hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of the human population — F_H.hMoI","title":"Size of the human population — F_H.hMoI","text":"Implements F_H hybrid MoI model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_H.hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of the human population — F_H.hMoI","text":"","code":"# S3 method for hMoI F_H(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/F_H.hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of the human population — F_H.hMoI","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_H.hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Size of the human population — F_H.hMoI","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_H.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of human population denominators — F_H","title":"Size of human population denominators — F_H","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_H.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of human population denominators — F_H","text":"","code":"F_H(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/F_H.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of human population denominators — F_H","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_H.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Size of human population denominators — F_H","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_H.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of the human population — F_H.trace","title":"Size of the human population — F_H.trace","text":"Implements F_H trace model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_H.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of the human population — F_H.trace","text":"","code":"# S3 method for trace F_H(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/F_H.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of the human population — F_H.trace","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_H.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Size of the human population — F_H.trace","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_alpha.basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of newly emerging adults from each larval habitat — F_alpha.basic","title":"Number of newly emerging adults from each larval habitat — F_alpha.basic","text":"Implements F_alpha basic competition model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_alpha.basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Number of newly emerging adults from each larval habitat — F_alpha.basic","text":"","code":"# S3 method for basic F_alpha(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/F_alpha.basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Number of newly emerging adults from each larval habitat — F_alpha.basic","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_alpha.basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Number of newly emerging adults from each larval habitat — F_alpha.basic","text":"numeric vector length nHabitats","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_alpha.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of newly emerging adults from each larval habitat — F_alpha","title":"Number of newly emerging adults from each larval habitat — F_alpha","text":"method dispatches type pars$Lpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_alpha.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Number of newly emerging adults from each larval habitat — F_alpha","text":"","code":"F_alpha(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/F_alpha.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Number of newly emerging adults from each larval habitat — F_alpha","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_alpha.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Number of newly emerging adults from each larval habitat — F_alpha","text":"numeric vector length nHabitats","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_alpha.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of newly emerging adults from each larval habitat — F_alpha.trace","title":"Number of newly emerging adults from each larval habitat — F_alpha.trace","text":"Implements F_alpha trace (forced emergence) model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_alpha.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Number of newly emerging adults from each larval habitat — F_alpha.trace","text":"","code":"# S3 method for trace F_alpha(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/F_alpha.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Number of newly emerging adults from each larval habitat — F_alpha.trace","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_alpha.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Number of newly emerging adults from each larval habitat — F_alpha.trace","text":"numeric vector length nHabitats","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_b.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Infection blocking pre-erythrocytic immunity — F_b.SIP","title":"Infection blocking pre-erythrocytic immunity — F_b.SIP","text":"Implements F_b SIP model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_b.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Infection blocking pre-erythrocytic immunity — F_b.SIP","text":"","code":"# S3 method for SIP F_b(y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/F_b.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Infection blocking pre-erythrocytic immunity — F_b.SIP","text":"y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_b.SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Infection blocking pre-erythrocytic immunity — F_b.SIP","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_b.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Infection blocking pre-erythrocytic immunity — F_b.SIS","title":"Infection blocking pre-erythrocytic immunity — F_b.SIS","text":"Implements F_b SIS model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_b.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Infection blocking pre-erythrocytic immunity — F_b.SIS","text":"","code":"# S3 method for SIS F_b(y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/F_b.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Infection blocking pre-erythrocytic immunity — F_b.SIS","text":"y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_b.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Infection blocking pre-erythrocytic immunity — F_b.SIS","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_b.hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Infection blocking pre-erythrocytic immunity — F_b.hMoI","title":"Infection blocking pre-erythrocytic immunity — F_b.hMoI","text":"Implements F_b hMoI model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_b.hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Infection blocking pre-erythrocytic immunity — F_b.hMoI","text":"","code":"# S3 method for hMoI F_b(y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/F_b.hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Infection blocking pre-erythrocytic immunity — F_b.hMoI","text":"y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_b.hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Infection 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index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_b.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Infection blocking pre-erythrocytic immunity — F_b","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_b.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Infection blocking pre-erythrocytic immunity — F_b.trace","title":"Infection blocking pre-erythrocytic immunity — F_b.trace","text":"Implements F_b trace model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_b.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Infection blocking pre-erythrocytic immunity — F_b.trace","text":"","code":"# S3 method for trace F_b(y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/F_b.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Infection blocking pre-erythrocytic immunity — F_b.trace","text":"y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_b.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Infection blocking pre-erythrocytic immunity — F_b.trace","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_beta.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute beta, the biting distribution matrix — F_beta","title":"Compute beta, the biting distribution matrix — F_beta","text":"Compute beta, biting distribution matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_beta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute beta, the biting distribution matrix — F_beta","text":"","code":"F_beta(H, W, wts_f, TaR)"},{"path":"https://dd-harp.github.io/exDE/reference/F_beta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute beta, the biting distribution matrix — F_beta","text":"H human / host population density W human / host availability patches wts_f blood feeding search weights TaR (time risk), matrix  dimensions nPatches nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_beta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute beta, the biting distribution matrix — F_beta","text":"matrix dimensions nStrata nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_eggs.GeRM.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of eggs laid by adult mosquitoes — F_eggs.GeRM","title":"Number of eggs laid by adult mosquitoes — F_eggs.GeRM","text":"Implements F_eggs GeRM 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nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_eggs.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of eggs laid by adult mosquitoes — F_eggs.RM","title":"Number of eggs laid by adult mosquitoes — F_eggs.RM","text":"Implements F_eggs RM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_eggs.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Number of eggs laid by adult mosquitoes — F_eggs.RM","text":"","code":"# S3 method for RM F_eggs(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/F_eggs.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Number of eggs laid by adult mosquitoes — F_eggs.RM","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_eggs.RM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Number of eggs laid by adult mosquitoes — F_eggs.RM","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_eggs.Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of eggs laid by adult mosquitoes — F_eggs.Ztrace","title":"Number of eggs laid by adult mosquitoes — F_eggs.Ztrace","text":"Implements F_eggs Ztrace model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_eggs.Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Number of eggs laid by adult mosquitoes — F_eggs.Ztrace","text":"","code":"# S3 method for Ztrace F_eggs(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/F_eggs.Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Number of eggs laid by adult mosquitoes — F_eggs.Ztrace","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_eggs.Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Number of eggs laid by adult mosquitoes — F_eggs.Ztrace","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_eggs.basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of eggs laid by adult mosquitoes — F_eggs.basicM","title":"Number of eggs laid by adult mosquitoes — F_eggs.basicM","text":"Implements F_eggs basic ecology model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_eggs.basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Number of eggs laid by adult mosquitoes — F_eggs.basicM","text":"","code":"# S3 method for basicM F_eggs(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/F_eggs.basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Number of eggs laid by adult mosquitoes — F_eggs.basicM","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_eggs.basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Number of eggs laid by adult mosquitoes — F_eggs.basicM","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_eggs.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of eggs laid by adult 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nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_f.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the blood feeding rate, f — F_f","title":"Compute the blood feeding rate, f — F_f","text":"method dispatches type MYZpar$f_par. set values bionomic parameters baseline values.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_f.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the blood feeding rate, f — F_f","text":"","code":"F_f(t, MYZpar)"},{"path":"https://dd-harp.github.io/exDE/reference/F_f.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the blood feeding rate, f — F_f","text":"t current simulation time MYZpar list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_f.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the blood feeding rate, f — F_f","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_f.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Static model for the blood feeding rate — F_f.static","title":"Static model for the blood feeding rate — F_f.static","text":"Implements F_f static model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_f.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Static model for the blood feeding rate — F_f.static","text":"","code":"# S3 method for static F_f(t, MYZpar)"},{"path":"https://dd-harp.github.io/exDE/reference/F_f.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Static model for the blood feeding rate — F_f.static","text":"t current simulation time MYZpar list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_f.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Static model for the blood feeding rate — F_f.static","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_f.type2.html","id":null,"dir":"Reference","previous_headings":"","what":"Type 2 functional response for the blood feeding rate — F_f.type2","title":"Type 2 functional response for the blood feeding rate — F_f.type2","text":"Implements F_f static model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_f.type2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Type 2 functional response for the blood feeding rate — F_f.type2","text":"","code":"# S3 method for type2 F_f(t, MYZpar)"},{"path":"https://dd-harp.github.io/exDE/reference/F_f.type2.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Type 2 functional response for the blood feeding rate — F_f.type2","text":"t current simulation time MYZpar list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_f.type2.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Type 2 functional response for the blood feeding rate — F_f.type2","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_foi.html","id":null,"dir":"Reference","previous_headings":"","what":"A model for daily FoI as a function of the daily EIR. — F_foi","title":"A model for daily FoI as a function of the daily EIR. — F_foi","text":"function compute daily local FoI function daily EIR effects partial immunity. computed based probabilistic model exposure possibly including environmental heterogeneity. model human / host infection terms describe partial immunity, e.g. affecting pre-erythrocytic immunity malaria called F_b, effects implemented . method dispatches type pars$FOIpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_foi.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A model for daily FoI as a function of the daily EIR. — F_foi","text":"","code":"F_foi(eir, b, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/F_foi.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A model for daily FoI as a function of the daily EIR. — F_foi","text":"eir daily eir stratum b probability infection, per bite pars model object list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_foi.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A model for daily FoI as a function of the daily EIR. — F_foi","text":"daily, local force infection numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_foi.nb.html","id":null,"dir":"Reference","previous_headings":"","what":"The daily FoI as a function 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list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_foi.nb.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"The daily FoI as a function of the daily EIR under a negative binomial model of exposure. — F_foi.nb","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_foi.pois.html","id":null,"dir":"Reference","previous_headings":"","what":"A Poisson model for the daily local FoI as a function of the daily EIR. — F_foi.pois","title":"A Poisson model for the daily local FoI as a function of the daily EIR. — F_foi.pois","text":"Implements F_foi Poisson model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_foi.pois.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A Poisson model for the daily local FoI as a function of the daily EIR. — F_foi.pois","text":"","code":"# S3 method for pois F_foi(eir, b, 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nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_fqM.Gtrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Blood feeding rate of the infective mosquito population — F_fqM.Gtrace","title":"Blood feeding rate of the infective mosquito population — F_fqM.Gtrace","text":"Implements F_fqM Gtrace model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_fqM.Gtrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Blood feeding rate of the infective mosquito population — F_fqM.Gtrace","text":"","code":"# S3 method for Gtrace F_fqM(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/F_fqM.Gtrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Blood feeding rate of the infective mosquito population — F_fqM.Gtrace","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_fqM.Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Blood feeding rate of the infective mosquito population — F_fqM.Gtrace","text":"numeric vector length nHabitats","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_fqM.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"The net blood feeding rate of the infective mosquito population in a patch — F_fqM.RM","title":"The net blood feeding rate of the infective mosquito population in a patch — F_fqM.RM","text":"Implements F_fqM RM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_fqM.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The net blood feeding rate of the infective mosquito population in a patch — F_fqM.RM","text":"","code":"# S3 method for RM F_fqM(t, y, pars, 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value(s).","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_nu.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the egg laying rate — F_nu","text":"","code":"F_nu(t, MYZpar)"},{"path":"https://dd-harp.github.io/exDE/reference/F_nu.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the egg laying rate — F_nu","text":"t current simulation time MYZpar list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_nu.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the egg laying rate — F_nu","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_nu.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Static model for the egg laying rate — F_nu.static","title":"Static model for the egg laying rate — F_nu.static","text":"Implements F_nu static 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nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_pr.hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the ","title":"Compute the ","text":"Implements F_pr hMoI model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_pr.hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the ","text":"","code":"# S3 method for hMoI F_pr(varslist, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/F_pr.hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the ","text":"varslist list variables attached name pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_pr.hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the ","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_pr.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the ","title":"Compute the ","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_pr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the ","text":"","code":"F_pr(varslist, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/F_pr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the ","text":"varslist list variables attached name pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_pr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the ","text":"numeric vector length 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for human blood fraction — F_q.dynamic","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_q.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the human blood fraction — F_q","title":"Compute the human blood fraction — F_q","text":"method dispatches type MYZpar$q_par. set values bionomic parameters baseline values.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_q.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the human blood fraction — F_q","text":"","code":"F_q(t, MYZpar)"},{"path":"https://dd-harp.github.io/exDE/reference/F_q.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the human blood fraction — F_q","text":"t current simulation time MYZpar 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MYZpar)"},{"path":"https://dd-harp.github.io/exDE/reference/F_sigma.BQS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Model for mosquito emigration based on resource availability — F_sigma.BQS","text":"t current simulation time MYZpar list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_sigma.BQS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Model for mosquito emigration based on resource availability — F_sigma.BQS","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_sigma.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute mosquito emigration rates — F_sigma","title":"Compute mosquito emigration rates — F_sigma","text":"method dispatches type MYZpar$sigma_par. set values sigma (possibly changing) baseline value(s).","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_sigma.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute mosquito emigration rates — F_sigma","text":"","code":"F_sigma(t, MYZpar)"},{"path":"https://dd-harp.github.io/exDE/reference/F_sigma.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute mosquito emigration rates — F_sigma","text":"t current simulation time MYZpar list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_sigma.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute mosquito emigration rates — F_sigma","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_sigma.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Static model for mosquito emigration — F_sigma.static","title":"Static model for mosquito emigration — F_sigma.static","text":"Implements F_sigma static model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_sigma.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Static model for mosquito emigration — F_sigma.static","text":"","code":"# S3 method for static F_sigma(t, MYZpar)"},{"path":"https://dd-harp.github.io/exDE/reference/F_sigma.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Static model for mosquito emigration — F_sigma.static","text":"t current simulation time MYZpar list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_sigma.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Static model for mosquito emigration — F_sigma.static","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_tau.html","id":null,"dir":"Reference","previous_headings":"","what":"Time spent host seeking/feeding and resting/ovipositing — F_tau","title":"Time spent host seeking/feeding and resting/ovipositing — F_tau","text":"method dispatches type pars$MYZpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_tau.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Time spent host seeking/feeding and resting/ovipositing — F_tau","text":"","code":"F_tau(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/F_tau.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Time spent host seeking/feeding and resting/ovipositing — F_tau","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_tau.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Time spent host seeking/feeding and resting/ovipositing — F_tau","text":"either numeric vector model supports feature, NULL","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_x.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of effective infectious human population — F_X.SIP","title":"Size of effective infectious human population — F_X.SIP","text":"Implements F_X SIP model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_x.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of effective infectious human population — F_X.SIP","text":"","code":"# S3 method for SIP F_X(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/F_x.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of effective infectious human population — F_X.SIP","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_x.SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Size of effective infectious human population — F_X.SIP","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_x.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of effective infectious human population — F_X.SIS","title":"Size of effective infectious human population — F_X.SIS","text":"Implements F_X SIS model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_x.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of effective infectious human population — F_X.SIS","text":"","code":"# S3 method for SIS F_X(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/F_x.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of effective infectious human population — F_X.SIS","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_x.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Size of effective infectious human population — F_X.SIS","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_x.hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of effective infectious human population — F_X.hMoI","title":"Size of effective infectious human population — F_X.hMoI","text":"Implements F_X hybrid MoI model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_x.hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of effective infectious human population — F_X.hMoI","text":"","code":"# S3 method for hMoI F_X(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/F_x.hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of effective infectious human population — F_X.hMoI","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_x.hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Size of effective infectious human population — F_X.hMoI","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_x.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of effective infectious human population — F_X","title":"Size of effective infectious human population — F_X","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_x.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of effective infectious human population — F_X","text":"","code":"F_X(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/F_x.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of effective infectious human population — F_X","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_x.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Size of effective infectious human population — F_X","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_x.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Size of effective infectious human population — F_X.trace","title":"Size of effective infectious human population — F_X.trace","text":"Implements F_X trace model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_x.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Size of effective infectious human population — F_X.trace","text":"","code":"# S3 method for trace F_X(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/F_x.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Size of effective infectious human population — F_X.trace","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/F_x.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Size of effective infectious human population — F_X.trace","text":"numeric vector length nStrata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HTC.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the HTC for the SIP model — HTC.SIP","title":"Compute the HTC for the SIP model — HTC.SIP","text":"Implements HTC SIP model demography.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HTC.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the HTC for the SIP model — HTC.SIP","text":"","code":"# S3 method for SIP HTC(pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/HTC.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the HTC for the SIP model — HTC.SIP","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HTC.SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the HTC for the SIP model — HTC.SIP","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HTC.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the HTC for the SIS model — HTC.SIS","title":"Compute the HTC for the SIS model — HTC.SIS","text":"Implements HTC SIS model demography.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HTC.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the HTC for the SIS model — HTC.SIS","text":"","code":"# S3 method for SIS HTC(pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/HTC.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the HTC for the SIS model — HTC.SIS","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HTC.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the HTC for the SIS model — HTC.SIS","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HTC.hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the HTC for the hMoI model — HTC.hMoI","title":"Compute the HTC for the hMoI model — HTC.hMoI","text":"Implements HTC hMoI model demography.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HTC.hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the HTC for the hMoI model — HTC.hMoI","text":"","code":"# S3 method for hMoI HTC(pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/HTC.hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the HTC for the hMoI model — HTC.hMoI","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HTC.hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the HTC for the hMoI model — HTC.hMoI","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HTC.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the human transmitting capacity — HTC","title":"Compute the human transmitting capacity — HTC","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HTC.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the human transmitting capacity — HTC","text":"","code":"HTC(pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/HTC.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the human transmitting capacity — HTC","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HTC.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the human transmitting capacity — HTC","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HabitatDynamics.html","id":null,"dir":"Reference","previous_headings":"","what":"Habitat Dynamics and Searching — HabitatDynamics","title":"Habitat Dynamics and Searching — HabitatDynamics","text":"Set values habitat search weights exogenous variables describing habitat_dynamics. method dispatches type pars$HABITAT_DYNAMICS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HabitatDynamics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Habitat Dynamics and Searching — HabitatDynamics","text":"","code":"HabitatDynamics(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/HabitatDynamics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Habitat Dynamics and Searching — HabitatDynamics","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HabitatDynamics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Habitat Dynamics and Searching — HabitatDynamics","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HabitatDynamics.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of habitat search weights and other exogenous variables describing habitat_dynamics — HabitatDynamics.static","title":"Set the values of habitat search weights and other exogenous variables describing habitat_dynamics — HabitatDynamics.static","text":"Implements HabitatDynamics static model habitat_dynamics (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HabitatDynamics.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of habitat search weights and other exogenous variables describing habitat_dynamics — HabitatDynamics.static","text":"","code":"# S3 method for static HabitatDynamics(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/HabitatDynamics.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of habitat search weights and other exogenous variables describing habitat_dynamics — HabitatDynamics.static","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/HabitatDynamics.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of habitat search weights and other exogenous variables describing habitat_dynamics — HabitatDynamics.static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Hydrology.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of exogenous variables describing hydrology — Hydrology","title":"Set the values of exogenous variables describing hydrology — Hydrology","text":"method dispatches type pars$HYDROLOGY.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Hydrology.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of exogenous variables describing hydrology — Hydrology","text":"","code":"Hydrology(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Hydrology.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of exogenous variables describing hydrology — Hydrology","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Hydrology.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of exogenous variables describing hydrology — Hydrology","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Hydrology.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of exogenous variables describing hydrology — Hydrology.null","title":"Set the values of exogenous variables describing hydrology — Hydrology.null","text":"Implements Hydrology null model hydrology (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Hydrology.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of exogenous variables describing hydrology — Hydrology.null","text":"","code":"# S3 method for null Hydrology(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Hydrology.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of exogenous variables describing hydrology — Hydrology.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Hydrology.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of exogenous variables describing hydrology — Hydrology.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/IRSeffectSizes.html","id":null,"dir":"Reference","previous_headings":"","what":"Model IRS effect sizes — IRSeffectSizes","title":"Model IRS effect sizes — IRSeffectSizes","text":"method dispatches type pars$IRS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/IRSeffectSizes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Model IRS effect sizes — IRSeffectSizes","text":"","code":"IRSeffectSizes(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/IRSeffectSizes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Model IRS effect sizes — IRSeffectSizes","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/IRSeffectSizes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Model IRS effect sizes — IRSeffectSizes","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/IRSeffectSizes.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Model IRS effect sizes — IRSeffectSizes.null","title":"Model IRS effect sizes — IRSeffectSizes.null","text":"method dispatches type pars$IRS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/IRSeffectSizes.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Model IRS effect sizes — IRSeffectSizes.null","text":"","code":"# S3 method for null IRSeffectSizes(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/IRSeffectSizes.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Model IRS effect sizes — IRSeffectSizes.null","text":"t current simulation time pars 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list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/IRSeffects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Model the effects of IRS — IRSeffects","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/IRSeffects.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Model the effects of IRS — IRSeffects.null","title":"Model the effects of IRS — IRSeffects.null","text":"method dispatches type pars$IRS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/IRSeffects.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Model the effects of IRS — IRSeffects.null","text":"","code":"# S3 method for null IRSeffects(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/IRSeffects.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Model the effects of IRS — IRSeffects.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/IRSeffects.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Model the effects of IRS — IRSeffects.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LBionomics.basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Reset aquatic parameters to baseline — LBionomics.basic","title":"Reset aquatic parameters to baseline — LBionomics.basic","text":"Implements LBionomics RM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LBionomics.basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reset aquatic parameters to baseline — LBionomics.basic","text":"","code":"# S3 method for basic LBionomics(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/LBionomics.basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reset aquatic parameters to baseline — LBionomics.basic","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LBionomics.basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reset aquatic parameters to baseline — LBionomics.basic","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LBionomics.html","id":null,"dir":"Reference","previous_headings":"","what":"Set aquatic bionomic parameter rates relative to baseline — LBionomics","title":"Set aquatic bionomic parameter rates relative to baseline — LBionomics","text":"method dispatches type pars$Lpar. compute values parameters function exogenous variables reset values bionomic parameters baseline values.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LBionomics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set aquatic bionomic parameter rates relative to baseline — LBionomics","text":"","code":"LBionomics(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/LBionomics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set aquatic bionomic parameter rates relative to baseline — LBionomics","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LBionomics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set aquatic bionomic parameter rates relative to baseline — LBionomics","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LBionomics.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Reset aquatic parameters to baseline — LBionomics.trace","title":"Reset aquatic parameters to baseline — LBionomics.trace","text":"Implements LBionomics RM 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LSMeffectSizes","title":"Compute effect sizes of LSM — LSMeffectSizes","text":"method dispatches type pars$LSM.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LSMeffectSizes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute effect sizes of LSM — LSMeffectSizes","text":"","code":"LSMeffectSizes(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/LSMeffectSizes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute effect sizes of LSM — LSMeffectSizes","text":"t current simulation time y state system pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LSMeffectSizes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute effect sizes of LSM — LSMeffectSizes","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LSMeffectSizes.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify effects of LSM, the null model — LSMeffectSizes.null","title":"Modify effects of LSM, the null model — LSMeffectSizes.null","text":"method dispatches type pars$LSM","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LSMeffectSizes.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify effects of LSM, the null model — LSMeffectSizes.null","text":"","code":"# S3 method for null LSMeffectSizes(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/LSMeffectSizes.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify effects of LSM, the null model — LSMeffectSizes.null","text":"t current simulation time y state system pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LSMeffectSizes.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify effects of LSM, the null model — LSMeffectSizes.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LSMeffects.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify effects of LSM — LSMeffects","title":"Modify effects of LSM — LSMeffects","text":"method dispatches type pars$LSM.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LSMeffects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify effects of LSM — LSMeffects","text":"","code":"LSMeffects(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/LSMeffects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify effects of LSM — LSMeffects","text":"t current simulation time y state system pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LSMeffects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify effects of LSM — LSMeffects","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LSMeffects.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify effects of LSM, the null model — LSMeffects.null","title":"Modify effects of LSM, the null model — LSMeffects.null","text":"method dispatches type pars$LSM","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LSMeffects.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify effects of LSM, the null model — LSMeffects.null","text":"","code":"# S3 method for null LSMeffects(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/LSMeffects.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify effects of LSM, the null model — LSMeffects.null","text":"t current simulation time y state system pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LSMeffects.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify effects of LSM, the null model — LSMeffects.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LocalFrac.dynamic.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute transmission terms dynamically, no update required — LocalFrac.dynamic","title":"Compute transmission terms dynamically, no update required — LocalFrac.dynamic","text":"method dispatches type pars$BFpar","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LocalFrac.dynamic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute transmission terms dynamically, no update required — LocalFrac.dynamic","text":"","code":"# S3 method for dynamic LocalFrac(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/LocalFrac.dynamic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute transmission terms dynamically, no update required — LocalFrac.dynamic","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LocalFrac.dynamic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute transmission terms dynamically, no update required — LocalFrac.dynamic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LocalFrac.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the local fraction — LocalFrac","title":"Compute the local fraction — LocalFrac","text":"method dispatches type pars$BFpar","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LocalFrac.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the local fraction — LocalFrac","text":"","code":"LocalFrac(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/LocalFrac.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the local fraction — LocalFrac","text":"pars, list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LocalFrac.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the local fraction — LocalFrac","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LocalFrac.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute transmission terms dynamically, no update required — LocalFrac.static","title":"Compute transmission terms dynamically, no update required — LocalFrac.static","text":"method dispatches type pars$BFpar","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LocalFrac.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute transmission terms dynamically, no update required — LocalFrac.static","text":"","code":"# S3 method for static LocalFrac(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/LocalFrac.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute transmission terms dynamically, no update required — LocalFrac.static","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/LocalFrac.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute transmission terms dynamically, no update required — LocalFrac.static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.GeRM.html","id":null,"dir":"Reference","previous_headings":"","what":"Reset bloodfeeding and mortality rates to baseline — MBionomics.GeRM","title":"Reset bloodfeeding and mortality rates to baseline — MBionomics.GeRM","text":"Implements MBionomics GeRM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.GeRM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reset bloodfeeding and mortality rates to baseline — MBionomics.GeRM","text":"","code":"# S3 method for GeRM MBionomics(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.GeRM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reset bloodfeeding and mortality rates to baseline — MBionomics.GeRM","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.GeRM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reset bloodfeeding and mortality rates to baseline — MBionomics.GeRM","text":"model list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.Gtrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute bloodfeeding and mortality rates — MBionomics.Gtrace","title":"Compute bloodfeeding and mortality rates — MBionomics.Gtrace","text":"Implements MBionomics Gtrace model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.Gtrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute bloodfeeding and mortality rates — MBionomics.Gtrace","text":"","code":"# S3 method for Gtrace MBionomics(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.Gtrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute bloodfeeding and mortality rates — MBionomics.Gtrace","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute bloodfeeding and mortality rates — MBionomics.Gtrace","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Reset bloodfeeding and mortality rates to baseline — MBionomics.RM","title":"Reset bloodfeeding and mortality rates to baseline — MBionomics.RM","text":"Implements MBionomics RM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reset bloodfeeding and mortality rates to baseline — MBionomics.RM","text":"","code":"# S3 method for RM MBionomics(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reset bloodfeeding and mortality rates to baseline — MBionomics.RM","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.RM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reset bloodfeeding and mortality rates to baseline — MBionomics.RM","text":"model list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute bloodfeeding and mortality rates — MBionomics.Ztrace","title":"Compute bloodfeeding and mortality rates — MBionomics.Ztrace","text":"Implements MBionomics Ztrace model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute bloodfeeding and mortality rates — MBionomics.Ztrace","text":"","code":"# S3 method for Ztrace MBionomics(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute bloodfeeding and mortality rates — MBionomics.Ztrace","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute bloodfeeding and mortality rates — MBionomics.Ztrace","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Set bionomic parameters to baseline — MBionomics.basicM","title":"Set bionomic parameters to baseline — MBionomics.basicM","text":"Implements MBionomics basicM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set bionomic parameters to baseline — MBionomics.basicM","text":"","code":"# S3 method for basicM MBionomics(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set bionomic parameters to baseline — MBionomics.basicM","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set bionomic parameters to baseline — MBionomics.basicM","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.html","id":null,"dir":"Reference","previous_headings":"","what":"Set bloodfeeding and mortality rates to baseline — MBionomics","title":"Set bloodfeeding and mortality rates to baseline — MBionomics","text":"method dispatches type pars$MYZpar. set values bionomic parameters baseline values.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set bloodfeeding and mortality rates to baseline — MBionomics","text":"","code":"MBionomics(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set bloodfeeding and mortality rates to baseline — MBionomics","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MBionomics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set bloodfeeding and mortality rates to baseline — MBionomics","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for mass medical — MassMedical.forced","title":"Methods for mass medical — MassMedical.forced","text":"Implements MassMedical","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for mass medical — MassMedical.forced","text":"","code":"# S3 method for forced MassMedical(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for mass medical — MassMedical.forced","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for mass medical — MassMedical.forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for mass medical interventions — MassMedical","title":"Methods for mass medical interventions — MassMedical","text":"method dispatches type pars$MASS_MED.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for mass medical interventions — MassMedical","text":"","code":"MassMedical(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for mass medical interventions — MassMedical","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for mass medical interventions — MassMedical","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for mass medical — MassMedical.null","title":"Methods for mass medical — MassMedical.null","text":"Implements MassMedical null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for mass medical — MassMedical.null","text":"","code":"# S3 method for null MassMedical(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for mass medical — MassMedical.null","text":"t current simulation time y state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/MassMedical.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for mass medical — MassMedical.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OtherBloodHosts.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts","title":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts","text":"method dispatches type pars$OTHER_BLOOD.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OtherBloodHosts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts","text":"","code":"OtherBloodHosts(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/OtherBloodHosts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OtherBloodHosts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OtherBloodHosts.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts.static","title":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts.static","text":"Implements OtherBloodHosts static model other_blood_hosts (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OtherBloodHosts.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts.static","text":"","code":"# S3 method for static OtherBloodHosts(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/OtherBloodHosts.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts.static","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OtherBloodHosts.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of exogenous variables describing other blood hosts — OtherBloodHosts.static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OviTraps.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for oviposition traps — OviTraps","title":"Methods for oviposition traps — OviTraps","text":"method dispatches type pars$OVITRAPS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OviTraps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for oviposition traps — OviTraps","text":"","code":"OviTraps(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/OviTraps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for oviposition traps — OviTraps","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OviTraps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for oviposition traps — OviTraps","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OviTraps.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for oviposition traps — OviTraps.null","title":"Methods for oviposition traps — OviTraps.null","text":"Implements OviTraps null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OviTraps.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for oviposition traps — OviTraps.null","text":"","code":"# S3 method for null OviTraps(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/OviTraps.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for oviposition traps — OviTraps.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OviTraps.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for oviposition traps — OviTraps.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OwnBedNet.html","id":null,"dir":"Reference","previous_headings":"","what":"Model bed net loss, called from Control(VectorControl) — OwnBedNet","title":"Model bed net loss, called from Control(VectorControl) — OwnBedNet","text":"method dispatches type pars$ITNown.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OwnBedNet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Model bed net loss, called from Control(VectorControl) — OwnBedNet","text":"","code":"OwnBedNet(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/OwnBedNet.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Model bed net loss, called from Control(VectorControl) — OwnBedNet","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OwnBedNet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Model bed net loss, called from Control(VectorControl) — OwnBedNet","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OwnBedNet.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Bed net ownership — OwnBedNet.null","title":"Bed net ownership — OwnBedNet.null","text":"Implements OwnBedNet null model bed nets (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OwnBedNet.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bed net ownership — OwnBedNet.null","text":"","code":"# S3 method for null OwnBedNet(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/OwnBedNet.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bed net ownership — OwnBedNet.null","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/OwnBedNet.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bed net ownership — OwnBedNet.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Rainfall.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing rainfall — Rainfall","title":"Methods for exogenous variables describing rainfall — Rainfall","text":"method dispatches type pars$RAINFALL.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Rainfall.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing rainfall — Rainfall","text":"","code":"Rainfall(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Rainfall.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing rainfall — Rainfall","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Rainfall.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing rainfall — Rainfall","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Rainfall.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing rainfall — Rainfall.null","title":"Methods for exogenous variables describing rainfall — Rainfall.null","text":"Implements Rainfall null model (variables)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Rainfall.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing rainfall — Rainfall.null","text":"","code":"# S3 method for null Rainfall(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Rainfall.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing rainfall — Rainfall.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Rainfall.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing rainfall — Rainfall.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Relative_Humidity.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing relative humidity — Relative_Humidity","title":"Methods for exogenous variables describing relative humidity — Relative_Humidity","text":"method dispatches type pars$HUMIDITY.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Relative_Humidity.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing relative humidity — Relative_Humidity","text":"","code":"Relative_Humidity(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Relative_Humidity.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing relative humidity — Relative_Humidity","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Relative_Humidity.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing relative humidity — Relative_Humidity","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Relative_Humidity.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing relative humidity — Relative_Humidity.null","title":"Methods for exogenous variables describing relative humidity — Relative_Humidity.null","text":"Implements Relative_Humidity null model (variables)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Relative_Humidity.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing relative humidity — Relative_Humidity.null","text":"","code":"# S3 method for null Relative_Humidity(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Relative_Humidity.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing relative humidity — Relative_Humidity.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Relative_Humidity.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing relative humidity — Relative_Humidity.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for resources — Resources.forced","title":"Methods for resources — Resources.forced","text":"Implements Resources","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for resources — Resources.forced","text":"","code":"# S3 method for forced Resources(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Resources.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for resources — Resources.forced","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for resources — Resources.forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of exogenous variables describing available mosquito resources — Resources","title":"Set the values of exogenous variables describing available mosquito resources — Resources","text":"method dispatches type pars$RESOURCES.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of exogenous variables describing available mosquito resources — Resources","text":"","code":"Resources(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Resources.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of exogenous variables describing available mosquito resources — Resources","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of exogenous variables describing available mosquito resources — Resources","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.setup.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify resources and resource availability — Resources.setup","title":"Modify resources and resource availability — Resources.setup","text":"Implements Resources null model resources","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.setup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify resources and resource availability — Resources.setup","text":"","code":"# S3 method for setup Resources(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Resources.setup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify resources and resource availability — Resources.setup","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.setup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify resources and resource availability — Resources.setup","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify resources and resource availability — Resources.static","title":"Modify resources and resource availability — Resources.static","text":"Implements Resources null model resources","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Resources.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify resources and resource availability — Resources.static","text":"","code":"# S3 method for static Resources(t, y, 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pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Shock.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up shocks — Shock","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Shock.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up shocks — Shock","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Shock.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up shocks — Shock.null","title":"Set up shocks — Shock.null","text":"Implements Shock null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Shock.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up shocks — Shock.null","text":"","code":"# S3 method for null Shock(t, 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method for null SprayHouses(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SprayHouses.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Do mass house spraying (IRS) — SprayHouses.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SprayHouses.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Do mass house spraying (IRS) — SprayHouses.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffectSizes.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes","title":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes","text":"method dispatches type pars$SUGAR_BAITS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffectSizes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes","text":"","code":"SugarBaitEffectSizes(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffectSizes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffectSizes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffectSizes.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes.null","title":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes.null","text":"method dispatches type pars$SUGAR_BAITS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffectSizes.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes.null","text":"","code":"# S3 method for null SugarBaitEffectSizes(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffectSizes.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes.null","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffectSizes.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for the effect sizes of the sugar baits — SugarBaitEffectSizes.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffects.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for the durability and effects of the sugar baits — SugarBaitEffects","title":"Methods for the durability and effects of the sugar baits — SugarBaitEffects","text":"method dispatches type pars$SUGAR_BAITS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for the durability and effects of the sugar baits — SugarBaitEffects","text":"","code":"SugarBaitEffects(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for the durability and effects of the sugar baits — SugarBaitEffects","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for the durability and effects of the sugar baits — SugarBaitEffects","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaitEffects.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for the effects of the sugar baits — SugarBaitEffects.null","title":"Methods for the effects of the sugar baits — SugarBaitEffects.null","text":"Implements SugarBaitEffects null model 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SugarBaitEffects.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaits.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for distributing sugar baits — SugarBaits","title":"Methods for distributing sugar baits — SugarBaits","text":"method dispatches type pars$SUGAR_BAITS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for distributing sugar baits — SugarBaits","text":"","code":"SugarBaits(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for distributing sugar baits — SugarBaits","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaits.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for distributing sugar baits — SugarBaits","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaits.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for sugar baits — SugarBaits.null","title":"Methods for sugar baits — SugarBaits.null","text":"Implements SugarBaits null model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaits.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for sugar baits — SugarBaits.null","text":"","code":"# S3 method for null SugarBaits(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaits.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for sugar baits — SugarBaits.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarBaits.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for sugar baits — SugarBaits.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarDynamics.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of exogenous variables describing sugar — SugarDynamics","title":"Set the values of exogenous variables describing sugar — SugarDynamics","text":"method dispatches type pars$SUGAR.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarDynamics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of exogenous variables describing sugar — SugarDynamics","text":"","code":"SugarDynamics(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SugarDynamics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of exogenous variables describing sugar — SugarDynamics","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarDynamics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of exogenous variables describing sugar — SugarDynamics","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarDynamics.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the values of exogenous variables describing sugar — SugarDynamics.static","title":"Set the values of exogenous variables describing sugar — SugarDynamics.static","text":"Implements SugarDynamics static model sugar (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarDynamics.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the values of exogenous variables describing sugar — SugarDynamics.static","text":"","code":"# S3 method for static SugarDynamics(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/SugarDynamics.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the values of exogenous variables describing sugar — SugarDynamics.static","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/SugarDynamics.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the values of exogenous variables describing sugar — SugarDynamics.static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Temperature.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing temperature — Temperature","title":"Methods for exogenous variables describing temperature — Temperature","text":"method dispatches type pars$TEMPERATURE.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Temperature.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing temperature — Temperature","text":"","code":"Temperature(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Temperature.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing temperature — Temperature","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Temperature.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing temperature — Temperature","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Temperature.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing temperature — Temperature.null","title":"Methods for exogenous variables describing temperature — Temperature.null","text":"Implements Temperature null model (variables)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Temperature.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing temperature — Temperature.null","text":"","code":"# S3 method for null Temperature(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Temperature.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing temperature — Temperature.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Temperature.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing temperature — Temperature.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.dynamic.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute transmission terms, the dynamic case — Transmission.dynamic","title":"Compute transmission terms, the dynamic case — Transmission.dynamic","text":"method dispatches type pars$BFpar","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.dynamic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute transmission terms, the dynamic case — Transmission.dynamic","text":"","code":"# S3 method for dynamic Transmission(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Transmission.dynamic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute transmission terms, the dynamic case — Transmission.dynamic","text":"t current simulation time y state vector pars 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pars$LSM","code":""},{"path":"https://dd-harp.github.io/exDE/reference/TreatHabitats.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the null model for LSM — TreatHabitats.null","text":"","code":"# S3 method for null TreatHabitats(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/TreatHabitats.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the null model for LSM — TreatHabitats.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/TreatHabitats.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the null model for LSM — TreatHabitats.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/UseBedNet.html","id":null,"dir":"Reference","previous_headings":"","what":"Model bed net usage, called from Behavior — UseBedNet","title":"Model bed net usage, called from Behavior — UseBedNet","text":"method dispatches type pars$ITNuse.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/UseBedNet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Model bed net usage, called from Behavior — UseBedNet","text":"","code":"UseBedNet(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/UseBedNet.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Model bed net usage, called from Behavior — UseBedNet","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/UseBedNet.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Model bed net usage, called from Behavior — UseBedNet","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/UseBedNet.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Bed net ownership — UseBedNet.null","title":"Bed net ownership — UseBedNet.null","text":"Implements UseBedNet null model bed nets (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/UseBedNet.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bed net ownership — UseBedNet.null","text":"","code":"# S3 method for null UseBedNet(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/UseBedNet.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bed net ownership — UseBedNet.null","text":"t current simulation time y vector state variables pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/UseBedNet.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bed net ownership — UseBedNet.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.control.html","id":null,"dir":"Reference","previous_headings":"","what":"Distribute vector control, the null model — VectorControl.control","title":"Distribute vector control, the null model — VectorControl.control","text":"Implements VectorControl control model vector control (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Distribute vector control, the null model — VectorControl.control","text":"","code":"# S3 method for control VectorControl(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Distribute vector control, the null model — VectorControl.control","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.control.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Distribute vector control, the null model — VectorControl.control","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.html","id":null,"dir":"Reference","previous_headings":"","what":"Distribute vector control — VectorControl","title":"Distribute vector control — VectorControl","text":"method dispatches type pars$VECTOR_CONTROL.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Distribute vector control — VectorControl","text":"","code":"VectorControl(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Distribute vector control — VectorControl","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Distribute vector control — VectorControl","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Distribute vector control — VectorControl.null","title":"Distribute vector control — VectorControl.null","text":"Implements VectorControl null model vector control (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Distribute vector control — VectorControl.null","text":"","code":"# S3 method for null VectorControl(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Distribute vector control — VectorControl.null","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControl.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Distribute vector control — VectorControl.null","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.control.html","id":null,"dir":"Reference","previous_headings":"","what":"Distribute vector control, the null model — VectorControlEffectSizes.control","title":"Distribute vector control, the null model — VectorControlEffectSizes.control","text":"Implements VectorControlEffectSizes control model vector control (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Distribute vector control, the null model — VectorControlEffectSizes.control","text":"","code":"# S3 method for control VectorControlEffectSizes(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Distribute vector control, the null model — VectorControlEffectSizes.control","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.control.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Distribute vector control, the null model — VectorControlEffectSizes.control","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.html","id":null,"dir":"Reference","previous_headings":"","what":"Vector control effect sizes — VectorControlEffectSizes","title":"Vector control effect sizes — VectorControlEffectSizes","text":"method dispatches type pars$VECTOR_CONTROL.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Vector control effect sizes — VectorControlEffectSizes","text":"","code":"VectorControlEffectSizes(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Vector control effect sizes — VectorControlEffectSizes","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Vector control effect sizes — VectorControlEffectSizes","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Vector control effect sizes — VectorControlEffectSizes.null","title":"Vector control effect sizes — VectorControlEffectSizes.null","text":"Implements VectorControlEffectSizes null model vector control (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Vector control effect sizes — VectorControlEffectSizes.null","text":"","code":"# S3 method for null VectorControlEffectSizes(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Vector control effect sizes — VectorControlEffectSizes.null","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffectSizes.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Vector control effect sizes — VectorControlEffectSizes.null","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.control.html","id":null,"dir":"Reference","previous_headings":"","what":"Vector control durability and effects — VectorControlEffects.control","title":"Vector control durability and effects — VectorControlEffects.control","text":"Implements VectorControlEffects control model vector control (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Vector control durability and effects — VectorControlEffects.control","text":"","code":"# S3 method for control VectorControlEffects(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Vector control durability and effects — VectorControlEffects.control","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.control.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Vector control durability and effects — VectorControlEffects.control","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.html","id":null,"dir":"Reference","previous_headings":"","what":"Vector control: durability & effects — VectorControlEffects","title":"Vector control: durability & effects — VectorControlEffects","text":"method dispatches type pars$VECTOR_CONTROL.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Vector control: durability & effects — VectorControlEffects","text":"","code":"VectorControlEffects(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Vector control: durability & effects — VectorControlEffects","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Vector control: durability & effects — VectorControlEffects","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Vector control: durability & effects — VectorControlEffects.null","title":"Vector control: durability & effects — VectorControlEffects.null","text":"Implements VectorControlEffects null model vector control (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Vector control: durability & effects — VectorControlEffects.null","text":"","code":"# S3 method for null VectorControlEffects(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Vector control: durability & effects — VectorControlEffects.null","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/VectorControlEffects.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Vector control: durability & effects — VectorControlEffects.null","text":"named list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Visitors, the basic model — Visitors.basic","title":"Visitors, the basic model — Visitors.basic","text":"Implements Visitors basic model Visitors","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Visitors, the basic model — Visitors.basic","text":"","code":"# S3 method for basic Visitors(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Visitors, the basic model — Visitors.basic","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Visitors, the basic model — Visitors.basic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.html","id":null,"dir":"Reference","previous_headings":"","what":"Visitors — Visitors","title":"Visitors — Visitors","text":"method dispatches type pars$VISITORS.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Visitors — Visitors","text":"","code":"Visitors(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Visitors — Visitors","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Visitors — Visitors","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Visitors, a static model — Visitors.static","title":"Visitors, a static model — Visitors.static","text":"Implements Visitors static model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Visitors, a static model — Visitors.static","text":"","code":"# S3 method for static Visitors(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Visitors, a static model — Visitors.static","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Visitors.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Visitors, a static model — Visitors.static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing weather — Weather.forced","title":"Methods for exogenous variables describing weather — Weather.forced","text":"Implements exogenous forcing Weather","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing weather — Weather.forced","text":"","code":"# S3 method for forced Weather(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Weather.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing weather — Weather.forced","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing weather — Weather.forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing weather — Weather","title":"Methods for exogenous variables describing weather — Weather","text":"method dispatches type pars$WEATHER.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing weather — Weather","text":"","code":"Weather(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Weather.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing weather — Weather","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing weather — Weather","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Methods for exogenous variables describing weather — Weather.null","title":"Methods for exogenous variables describing weather — Weather.null","text":"Implements Weather null model (variables)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Methods for exogenous variables describing weather — Weather.null","text":"","code":"# S3 method for null Weather(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/Weather.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Methods for exogenous variables describing weather — Weather.null","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/Weather.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Methods for exogenous variables describing weather — Weather.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/approx_equal.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if two numeric values are approximately equal — approx_equal","title":"Check if two numeric values are approximately equal — approx_equal","text":"Check two numeric values approximately equal","code":""},{"path":"https://dd-harp.github.io/exDE/reference/approx_equal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if two numeric values are approximately equal — approx_equal","text":"","code":"approx_equal(a, b, tol = sqrt(.Machine$double.eps))"},{"path":"https://dd-harp.github.io/exDE/reference/approx_equal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if two numeric values are approximately equal — approx_equal","text":"numeric object b numeric object tol numeric tolerance","code":""},{"path":"https://dd-harp.github.io/exDE/reference/approx_equal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if two numeric values are approximately equal — approx_equal","text":"logical value","code":""},{"path":"https://dd-harp.github.io/exDE/reference/checkIt.html","id":null,"dir":"Reference","previous_headings":"","what":"Check the length of an input value — checkIt","title":"Check the length of an input value — checkIt","text":"Check length input value","code":""},{"path":"https://dd-harp.github.io/exDE/reference/checkIt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check the length of an input value — checkIt","text":"","code":"checkIt(x, lng, type = \"numeric\", fixit = TRUE)"},{"path":"https://dd-harp.github.io/exDE/reference/checkIt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check the length of an input value — checkIt","text":"x numeric object lng numeric object type character string specifying required typeof fixit logical value, TRUE force length lng","code":""},{"path":"https://dd-harp.github.io/exDE/reference/checkIt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check the length of an input value — checkIt","text":"numeric object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Check abiotic — check_abiotic.forced","title":"Check abiotic — check_abiotic.forced","text":"Check abiotic","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check abiotic — check_abiotic.forced","text":"","code":"# S3 method for forced check_abiotic(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check abiotic — check_abiotic.forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check abiotic — check_abiotic.forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.html","id":null,"dir":"Reference","previous_headings":"","what":"Check abiotic — check_abiotic","title":"Check abiotic — check_abiotic","text":"Check abiotic","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check abiotic — check_abiotic","text":"","code":"check_abiotic(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check abiotic — check_abiotic","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check abiotic — check_abiotic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Check abiotic — check_abiotic.null","title":"Check abiotic — check_abiotic.null","text":"Check abiotic","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check abiotic — check_abiotic.null","text":"","code":"# S3 method for null check_abiotic(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check abiotic — check_abiotic.null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_abiotic.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check abiotic — check_abiotic.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Check civil — check_civil.forced","title":"Check civil — check_civil.forced","text":"Check civil","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check civil — check_civil.forced","text":"","code":"# S3 method for forced check_civil(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check civil — check_civil.forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check civil — check_civil.forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.html","id":null,"dir":"Reference","previous_headings":"","what":"Check civil — check_civil","title":"Check civil — check_civil","text":"Check civil","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check civil — check_civil","text":"","code":"check_civil(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check civil — check_civil","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check civil — check_civil","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.null.html","id":null,"dir":"Reference","previous_headings":"","what":"Check civil — check_civil.null","title":"Check civil — check_civil.null","text":"Check civil","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check civil — check_civil.null","text":"","code":"# S3 method for null check_civil(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check civil — check_civil.null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/check_civil.null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check civil — check_civil.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_AvailableHabitat.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute total availability of aquatic habitats — compute_AvailableHabitat","title":"Compute total availability of aquatic habitats — compute_AvailableHabitat","text":"Computes availability aquatic habitats","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_AvailableHabitat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute total availability of aquatic habitats — compute_AvailableHabitat","text":"","code":"compute_AvailableHabitat(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_AvailableHabitat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute total availability of aquatic habitats — compute_AvailableHabitat","text":"pars list s vector species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_AvailableHabitat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute total availability of aquatic habitats — compute_AvailableHabitat","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_AvailableHosts.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute availability blood hosts of the i^th species — compute_AvailableHosts","title":"Compute availability blood hosts of the i^th species — compute_AvailableHosts","text":"Compute availability pathogen's hosts blood feeding","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_AvailableHosts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute availability blood hosts of the i^th species — compute_AvailableHosts","text":"","code":"compute_AvailableHosts(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_AvailableHosts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute availability blood hosts of the i^th species — compute_AvailableHosts","text":"t current simulation time y state vector pars list s vector species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_AvailableHosts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute availability blood hosts of the i^th species — compute_AvailableHosts","text":"numeric vector length nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute EIR — compute_EIR","title":"Compute EIR — compute_EIR","text":"function computes EIR stratum host species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute EIR — compute_EIR","text":"","code":"compute_EIR(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_EIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute EIR — compute_EIR","text":"t current simulation time y state vector pars, list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EIR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute EIR — compute_EIR","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EIR_full.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute EIR for each vector-host pair — compute_EIR_full","title":"Compute EIR for each vector-host pair — compute_EIR_full","text":"function computes EIR vector species stratum host species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EIR_full.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute EIR for each vector-host pair — compute_EIR_full","text":"","code":"compute_EIR_full(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_EIR_full.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute EIR for each vector-host pair — compute_EIR_full","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EIR_full.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute EIR for each vector-host pair — compute_EIR_full","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EggsLaid.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute eggs laid — compute_EggsLaid","title":"Compute eggs laid — compute_EggsLaid","text":"Computes eggs laid s^th species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EggsLaid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute eggs laid — compute_EggsLaid","text":"","code":"compute_EggsLaid(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_EggsLaid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute eggs laid — compute_EggsLaid","text":"t time y state variables pars model object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_EggsLaid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute eggs laid — compute_EggsLaid","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_NI.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the NI — compute_NI","title":"Compute the NI — compute_NI","text":"Using output deSolve::ode deSolve::dede, compute NI stratum","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_NI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the NI — compute_NI","text":"","code":"compute_NI(deout, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_NI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the NI — compute_NI","text":"deout matrix, output deSolve pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_NI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the NI — compute_NI","text":"numeric containing NI","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_NI_ix.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute NI once — compute_NI_ix","title":"Compute NI once — compute_NI_ix","text":"Using output deSolve::ode deSolve::dede, compute NI point time","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_NI_ix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute NI once — compute_NI_ix","text":"","code":"compute_NI_ix(ix, deout, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_NI_ix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute NI once — compute_NI_ix","text":"ix integer deout matrix, output deSolve pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_NI_ix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute NI once — compute_NI_ix","text":"list containing NI","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_beta.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute beta — compute_beta","title":"Compute beta — compute_beta","text":"function computes mixing matrix, beta","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_beta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute beta — compute_beta","text":"","code":"compute_beta(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_beta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute beta — compute_beta","text":"t current simulation time y state vector pars, list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_beta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute beta — compute_beta","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_calU.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute calU — compute_calU","title":"Compute calU — compute_calU","text":"Computes egg laying matrices","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_calU.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute calU — compute_calU","text":"","code":"compute_calU(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_calU.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute calU — compute_calU","text":"t time y state variables pars model object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_calU.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute calU — compute_calU","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqM.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the fqM — compute_fqM","title":"Compute the fqM — compute_fqM","text":"Using output deSolve::ode deSolve::dede, compute fqM every point time","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the fqM — compute_fqM","text":"","code":"compute_fqM(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the fqM — compute_fqM","text":"deout matrix, output deSolve pars list s vector species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the fqM — compute_fqM","text":"vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqM_ix.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the fqM for the ith — compute_fqM_ix","title":"Compute the fqM for the ith — compute_fqM_ix","text":"Using output deSolve::ode deSolve::dede, compute fqM one point time","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqM_ix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the fqM for the ith — compute_fqM_ix","text":"","code":"compute_fqM_ix(ix, deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqM_ix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the fqM for the ith — compute_fqM_ix","text":"ix integer deout matrix, output deSolve pars list s vector species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqM_ix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the fqM for the ith — compute_fqM_ix","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the fqZ — compute_fqZ","title":"Compute the fqZ — compute_fqZ","text":"Using output deSolve::ode deSolve::dede, compute fqZ every point time","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the fqZ — compute_fqZ","text":"","code":"compute_fqZ(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the fqZ — compute_fqZ","text":"deout matrix, output deSolve pars list s vector species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqZ.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the fqZ — compute_fqZ","text":"vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqZ_ix.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the fqZ for the ith — compute_fqZ_ix","title":"Compute the fqZ for the ith — compute_fqZ_ix","text":"Using output deSolve::ode deSolve::dede, compute fqZ one point time","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqZ_ix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the fqZ for the ith — compute_fqZ_ix","text":"","code":"compute_fqZ_ix(ix, deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqZ_ix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the fqZ for the ith — compute_fqZ_ix","text":"ix integer deout matrix, output deSolve pars list s vector species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_fqZ_ix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the fqZ for the ith — compute_fqZ_ix","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_kappa.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute kappa — compute_kappa","title":"Compute kappa — compute_kappa","text":"function computes kappa vector species patch","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_kappa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute kappa — compute_kappa","text":"","code":"compute_kappa(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_kappa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute kappa — compute_kappa","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_kappa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute kappa — compute_kappa","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_local_frac.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the local fraction — compute_local_frac","title":"Compute the local fraction — compute_local_frac","text":"Compute availability pathogen's hosts blood feeding","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_local_frac.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the local fraction — compute_local_frac","text":"","code":"compute_local_frac(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_local_frac.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the local fraction — compute_local_frac","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_local_frac.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the local fraction — compute_local_frac","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.cohort.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute dynamical terms — compute_terms.cohort","title":"Compute dynamical terms — compute_terms.cohort","text":"Using output deSolve compute dynamical terms output xde_solve.cohort","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.cohort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute dynamical terms — compute_terms.cohort","text":"","code":"# S3 method for cohort compute_terms(varslist, deout, pars, s, i)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.cohort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute dynamical terms — compute_terms.cohort","text":"varslist list variable names attached deout matrix, output deSolve pars list s vector species index host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.cohort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute dynamical terms — compute_terms.cohort","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute dynamical terms — compute_terms","title":"Compute dynamical terms — compute_terms","text":"Using output deSolve compute dynamical terms every point time. method dispatches type pars$compute.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute dynamical terms — compute_terms","text":"","code":"compute_terms(varslist, deout, pars, s, i)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute dynamical terms — compute_terms","text":"varslist list variable names attached deout matrix, output deSolve pars list s vector species index host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute dynamical terms — compute_terms","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.human.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute dynamical terms — compute_terms.human","title":"Compute dynamical terms — compute_terms.human","text":"Using output deSolve compute dynamical terms output xde_solve.human","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.human.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute dynamical terms — compute_terms.human","text":"","code":"# S3 method for human compute_terms(varslist, deout, pars, s, i)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.human.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute dynamical terms — compute_terms.human","text":"varslist list variable names attached deout matrix, output deSolve pars list s vector species index host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.human.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute dynamical terms — compute_terms.human","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.na.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute dynamical terms — compute_terms.na","title":"Compute dynamical terms — compute_terms.na","text":"Using output deSolve compute dynamical terms output xde_solve relevant dynamical terms","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute dynamical terms — compute_terms.na","text":"","code":"# S3 method for na compute_terms(varslist, deout, pars, s, i)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute dynamical terms — compute_terms.na","text":"varslist list variable names attached deout matrix, output deSolve pars list s vector species index host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute dynamical terms — compute_terms.na","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.xde.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute dynamical terms — compute_terms.xde","title":"Compute dynamical terms — compute_terms.xde","text":"Using output deSolve compute dynamical terms output xde_solve.ode xde_solve.dde","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.xde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute dynamical terms — compute_terms.xde","text":"","code":"# S3 method for xde compute_terms(varslist, deout, pars, s, i)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.xde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute dynamical terms — compute_terms.xde","text":"varslist list variable names attached deout matrix, output deSolve pars list s vector species index host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms.xde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute dynamical terms — compute_terms.xde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms_steady.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute dynamical terms — compute_terms_steady","title":"Compute dynamical terms — compute_terms_steady","text":"Using output deSolve compute dynamical terms output root_solve","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms_steady.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute dynamical terms — compute_terms_steady","text":"","code":"compute_terms_steady(varslist, y_eq, pars, s, i)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms_steady.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute dynamical terms — compute_terms_steady","text":"varslist list variable names attached y_eq matrix, output rootSolve pars list s vector species index host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_terms_steady.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute dynamical terms — compute_terms_steady","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_aqua.html","id":null,"dir":"Reference","previous_headings":"","what":"Differential equation models for aquatic mosquito populations — compute_vars_aqua","title":"Differential equation models for aquatic mosquito populations — compute_vars_aqua","text":"Compute everything derivatives aquatic mosquito-differential equation model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_aqua.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Differential equation models for aquatic mosquito populations — compute_vars_aqua","text":"","code":"compute_vars_aqua(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_aqua.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Differential equation models for aquatic mosquito populations — compute_vars_aqua","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_aqua.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Differential equation models for aquatic mosquito populations — compute_vars_aqua","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_cohort.html","id":null,"dir":"Reference","previous_headings":"","what":"Differential equation models for human cohorts — compute_vars_cohort","title":"Differential equation models for human cohorts — compute_vars_cohort","text":"Compute everything derivatives human cohort differential equation model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_cohort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Differential equation models for human cohorts — compute_vars_cohort","text":"","code":"compute_vars_cohort(a, y, pars, F_eir)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_cohort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Differential equation models for human cohorts — compute_vars_cohort","text":"age cohort y state vector pars list F_eir trace function returns eir","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_cohort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Differential equation models for human cohorts — compute_vars_cohort","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_full.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute other variables at time t — compute_vars_full","title":"Compute other variables at time t — compute_vars_full","text":"Compute everything derivatives generalized spatial differential equation model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_full.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute other variables at time t — compute_vars_full","text":"","code":"compute_vars_full(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_full.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute other variables at time t — compute_vars_full","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_full.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute other variables at time t — compute_vars_full","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_human.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute other variables at time t — compute_vars_human","title":"Compute other variables at time t — compute_vars_human","text":"Compute everything derivatives human-differential equation model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_human.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute other variables at time t — compute_vars_human","text":"","code":"compute_vars_human(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_human.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute other variables at time t — compute_vars_human","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_human.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute other variables at time t — compute_vars_human","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_mosy.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute other variables at time t — compute_vars_mosy","title":"Compute other variables at time t — compute_vars_mosy","text":"Compute everything derivatives mosquito-differential equation model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_mosy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute other variables at time t — compute_vars_mosy","text":"","code":"compute_vars_mosy(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_mosy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute other variables at time t — compute_vars_mosy","text":"t current simulation time y state vector pars list appropriate adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/compute_vars_mosy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute other variables at time t — compute_vars_mosy","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dEIPdt.html","id":null,"dir":"Reference","previous_headings":"","what":"Compute the derivative of the EIP as a function of time — dEIPdt","title":"Compute the derivative of the EIP as a function of time — dEIPdt","text":"method dispatches type EIPmod.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dEIPdt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compute the derivative of the EIP as a function of time — dEIPdt","text":"","code":"dEIPdt(t, EIPmod)"},{"path":"https://dd-harp.github.io/exDE/reference/dEIPdt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compute the derivative of the EIP as a function of time — dEIPdt","text":"t current simulation time EIPmod list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dEIPdt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compute the derivative of the EIP as a function of time — dEIPdt","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dEIPdt.static.html","id":null,"dir":"Reference","previous_headings":"","what":"This function computes the negative derivative of the EIP as a function of time — dEIPdt.static","title":"This function computes the negative derivative of the EIP as a function of time — dEIPdt.static","text":"Implements dEIPdt static model (dEIPdt=0)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dEIPdt.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"This function computes the negative derivative of the EIP as a function of time — dEIPdt.static","text":"","code":"# S3 method for static dEIPdt(t, EIPmod)"},{"path":"https://dd-harp.github.io/exDE/reference/dEIPdt.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"This function computes the negative derivative of the EIP as a function of time — dEIPdt.static","text":"t current simulation time EIPmod list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dEIPdt.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"This function computes the negative derivative of the EIP as a function of time — dEIPdt.static","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dHdt.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives of demographic changes in human populations — dHdt","title":"Derivatives of demographic changes in human populations — dHdt","text":"method dispatches type pars$Hpar$dH","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dHdt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives of demographic changes in human populations — dHdt","text":"","code":"dHdt(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/dHdt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives of demographic changes in human populations — dHdt","text":"t current simulation time y state vector pars list index host species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dHdt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives of demographic changes in human populations — dHdt","text":"see help pages specific methods","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dHdt.zero.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives of demographic changes in human populations — dHdt.zero","title":"Derivatives of demographic changes in human populations — dHdt.zero","text":"Implements dHdt y static","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dHdt.zero.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives of demographic changes in human populations — dHdt.zero","text":"","code":"# S3 method for zero dHdt(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/dHdt.zero.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives of demographic changes in human populations — dHdt.zero","text":"t current simulation time y state vector pars list index host species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dHdt.zero.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives of demographic changes in human populations — dHdt.zero","text":"numeric vector 0s","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for aquatic stage mosquitoes — dLdt.basic","title":"Derivatives for aquatic stage mosquitoes — dLdt.basic","text":"Implements dLdt basic competition model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for aquatic stage mosquitoes — dLdt.basic","text":"","code":"# S3 method for basic dLdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for aquatic stage mosquitoes — dLdt.basic","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for aquatic stage mosquitoes — dLdt.basic","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for aquatic stage mosquitoes — dLdt","title":"Derivatives for aquatic stage mosquitoes — dLdt","text":"method dispatches type pars$Lpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for aquatic stage mosquitoes — dLdt","text":"","code":"dLdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for aquatic stage mosquitoes — dLdt","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for aquatic stage mosquitoes — dLdt","text":"numeric vector length pars$L_ix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for aquatic stage mosquitoes — dLdt.trace","title":"Derivatives for aquatic stage mosquitoes — dLdt.trace","text":"Implements dLdt trace (forced emergence) model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for aquatic stage mosquitoes — dLdt.trace","text":"","code":"# S3 method for trace dLdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for aquatic stage mosquitoes — dLdt.trace","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dLdt.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for aquatic stage mosquitoes — dLdt.trace","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.GeRM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for adult mosquitoes — dMYZdt.GeRM_dde","title":"Derivatives for adult mosquitoes — dMYZdt.GeRM_dde","text":"Implements dMYZdt GeRM DDE model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.GeRM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for adult mosquitoes — dMYZdt.GeRM_dde","text":"","code":"# S3 method for GeRM_dde dMYZdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.GeRM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for adult mosquitoes — dMYZdt.GeRM_dde","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.GeRM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for adult mosquitoes — dMYZdt.GeRM_dde","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.GeRM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for adult mosquitoes — dMYZdt.GeRM_ode","title":"Derivatives for adult mosquitoes — dMYZdt.GeRM_ode","text":"Implements dMYZdt GeRM ODE model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.GeRM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for adult mosquitoes — dMYZdt.GeRM_ode","text":"","code":"# S3 method for GeRM_ode dMYZdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.GeRM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for adult mosquitoes — dMYZdt.GeRM_ode","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.GeRM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for adult mosquitoes — dMYZdt.GeRM_ode","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.Gtrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for aquatic stage mosquitoes — dMYZdt.Gtrace","title":"Derivatives for aquatic stage mosquitoes — dMYZdt.Gtrace","text":"Implements dMYZdt Gtrace (forced emergence) model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.Gtrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for aquatic stage mosquitoes — dMYZdt.Gtrace","text":"","code":"# S3 method for Gtrace dMYZdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.Gtrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for aquatic stage mosquitoes — dMYZdt.Gtrace","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for aquatic stage mosquitoes — dMYZdt.Gtrace","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.RM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for adult mosquitoes — dMYZdt.RM_dde","title":"Derivatives for adult mosquitoes — dMYZdt.RM_dde","text":"Implements dMYZdt RM DDE model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.RM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for adult mosquitoes — dMYZdt.RM_dde","text":"","code":"# S3 method for RM_dde dMYZdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.RM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for adult mosquitoes — dMYZdt.RM_dde","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.RM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for adult mosquitoes — dMYZdt.RM_dde","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.RM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for adult mosquitoes — dMYZdt.RM_ode","title":"Derivatives for adult mosquitoes — dMYZdt.RM_ode","text":"Implements dMYZdt RM ODE model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.RM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for adult mosquitoes — dMYZdt.RM_ode","text":"","code":"# S3 method for RM_ode dMYZdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.RM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for adult mosquitoes — dMYZdt.RM_ode","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.RM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for adult mosquitoes — dMYZdt.RM_ode","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for aquatic stage mosquitoes — dMYZdt.Ztrace","title":"Derivatives for aquatic stage mosquitoes — dMYZdt.Ztrace","text":"Implements dMYZdt Ztrace (forced emergence) model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for aquatic stage mosquitoes — dMYZdt.Ztrace","text":"","code":"# S3 method for Ztrace dMYZdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for aquatic stage mosquitoes — dMYZdt.Ztrace","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for aquatic stage mosquitoes — dMYZdt.Ztrace","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for adult mosquitoes — dMYZdt.basicM","title":"Derivatives for adult mosquitoes — dMYZdt.basicM","text":"Implements dMYZdt basicM ODE model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for adult mosquitoes — dMYZdt.basicM","text":"","code":"# S3 method for basicM dMYZdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for adult mosquitoes — dMYZdt.basicM","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for adult mosquitoes — dMYZdt.basicM","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for adult mosquitoes — dMYZdt","title":"Derivatives for adult mosquitoes — dMYZdt","text":"method dispatches type pars$MYZpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for adult mosquitoes — dMYZdt","text":"","code":"dMYZdt(t, y, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for adult mosquitoes — dMYZdt","text":"t current simulation time y state vector pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dMYZdt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for adult mosquitoes — dMYZdt","text":"derivatives vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.SIP","title":"Derivatives for human population — dXdt.SIP","text":"Implements dXdt SIP model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.SIP","text":"","code":"# S3 method for SIP dXdt(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.SIP","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.SIP","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.SIS","title":"Derivatives for human population — dXdt.SIS","text":"Implements dXdt SIS model, demography.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.SIS","text":"","code":"# S3 method for SIS dXdt(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.SIS","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.SIS","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.hMoI","title":"Derivatives for human population — dXdt.hMoI","text":"Implements dXdt hybrid MoI model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.hMoI","text":"","code":"# S3 method for hMoI dXdt(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.hMoI","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.hMoI","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt","title":"Derivatives for human population — dXdt","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt","text":"","code":"dXdt(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Derivatives for human population — dXdt.trace","title":"Derivatives for human population — dXdt.trace","text":"Implements dXdt trace model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Derivatives for human population — dXdt.trace","text":"","code":"# S3 method for trace dXdt(t, y, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Derivatives for human population — dXdt.trace","text":"t current simulation time y state vector pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dXdt.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Derivatives for human population — dXdt.trace","text":"numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dde2ode_MYZ.dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a model from dde to the corresponding ode — dde2ode_MYZ.dde","title":"Convert a model from dde to the corresponding ode — dde2ode_MYZ.dde","text":"dde, return corresponding ode","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dde2ode_MYZ.dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a model from dde to the corresponding ode — dde2ode_MYZ.dde","text":"","code":"# S3 method for dde dde2ode_MYZ(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/dde2ode_MYZ.dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a model from dde to the corresponding ode — dde2ode_MYZ.dde","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dde2ode_MYZ.dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a model from dde to the corresponding ode — dde2ode_MYZ.dde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/dde2ode_MYZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a model from dde to the corresponding ode — dde2ode_MYZ","title":"Convert a model from dde to the corresponding ode — dde2ode_MYZ","text":"method dispatches type 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s)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.GeRM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_MYZ.GeRM_dde","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.GeRM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_MYZ.GeRM_dde","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.GeRM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_MYZ.GeRM_ode","title":"Return initial values as a vector — get_inits_MYZ.GeRM_ode","text":"Implements get_inits_MYZ GeRM 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get_inits_MYZ.Gtrace","title":"Return initial values as a vector — get_inits_MYZ.Gtrace","text":"Implements get_inits_MYZ GeRM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.Gtrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_MYZ.Gtrace","text":"","code":"# S3 method for Gtrace get_inits_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.Gtrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_MYZ.Gtrace","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_MYZ.Gtrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.RM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_MYZ.RM_dde","title":"Return initial values as a vector — get_inits_MYZ.RM_dde","text":"Implements get_inits_MYZ RM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.RM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_MYZ.RM_dde","text":"","code":"# S3 method for RM_dde get_inits_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.RM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_MYZ.RM_dde","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.RM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_MYZ.RM_dde","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.RM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_MYZ.RM_ode","title":"Return initial values as a vector — get_inits_MYZ.RM_ode","text":"Implements get_inits_MYZ RM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.RM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_MYZ.RM_ode","text":"","code":"# S3 method for RM_ode get_inits_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.RM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_MYZ.RM_ode","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.RM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_MYZ.RM_ode","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_MYZ.Ztrace","title":"Return initial values as a vector — get_inits_MYZ.Ztrace","text":"Implements get_inits_MYZ GeRM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return 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get_inits_MYZ","title":"Return initial values as a vector — get_inits_MYZ","text":"method dispatches type pars$MYZpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_MYZ","text":"","code":"get_inits_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_MYZ","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_MYZ.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return initial values as a vector — get_inits_MYZ","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Return 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get_inits_X.SIP","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Return initial values as a vector — get_inits_X.SIS","title":"Return initial values as a vector — get_inits_X.SIS","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return initial values as a vector — get_inits_X.SIS","text":"","code":"# S3 method for SIS get_inits_X(pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/get_inits_X.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return initial values as a vector — get_inits_X.SIS","text":"pars list host species 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simulation","code":""},{"path":"https://dd-harp.github.io/exDE/reference/last_to_inits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the initial values to the last values of the last simulation — last_to_inits","text":"","code":"last_to_inits(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/last_to_inits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the initial values to the last values of the last simulation — last_to_inits","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/last_to_inits.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the initial values to the last values of the last simulation — last_to_inits","text":"y numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Hpar_trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for human null model — make_Hpar_trace","title":"Make parameters for human null model — make_Hpar_trace","text":"Make parameters human null model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Hpar_trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for human null model — make_Hpar_trace","text":"","code":"make_Hpar_trace(nPatches, Hopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_Hpar_trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for human null model — make_Hpar_trace","text":"nPatches number patches model Hopts list overwrite defaults","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Hpar_trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for human null model — make_Hpar_trace","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Linits_basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for basic competition aquatic mosquito model — make_Linits_basic","title":"Make inits for basic competition aquatic mosquito model — make_Linits_basic","text":"Make inits basic competition aquatic mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Linits_basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for basic competition aquatic mosquito model — make_Linits_basic","text":"","code":"make_Linits_basic(nHabitats, Lopts = list(), L0 = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Linits_basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for basic competition aquatic mosquito model — make_Linits_basic","text":"nHabitats number habitats model Lopts list overwrites default values L0 initial conditions","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Linits_basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for basic competition aquatic mosquito model — make_Linits_basic","text":"list Linits added","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Lpar_basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for basic competition aquatic mosquito model — make_Lpar_basic","title":"Make parameters for basic competition aquatic mosquito model — make_Lpar_basic","text":"Make parameters basic competition aquatic mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Lpar_basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for basic competition aquatic mosquito model — make_Lpar_basic","text":"","code":"make_Lpar_basic(nHabitats, Lopts = list(), psi = 1/8, phi = 1/8, theta = 1/100)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Lpar_basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for basic competition aquatic mosquito model — make_Lpar_basic","text":"nHabitats number habitats model Lopts list overwrites default values psi maturation rates aquatic habitat phi density-independent mortality rates aquatic habitat theta density-dependent mortality terms aquatic habitat","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Lpar_basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for basic competition aquatic mosquito model — make_Lpar_basic","text":"list Lpar added","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Lpar_trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for trace aquatic mosquito model — make_Lpar_trace","title":"Make parameters for trace aquatic mosquito model — make_Lpar_trace","text":"Make parameters trace aquatic mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Lpar_trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for trace aquatic mosquito model — make_Lpar_trace","text":"","code":"make_Lpar_trace(nHabitats, Lopts = list(), Lambda = 1000, Lt = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Lpar_trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for trace aquatic mosquito model — make_Lpar_trace","text":"nHabitats number habitats model Lopts list overwrites default values Lambda vector mean emergence rates aquatic habitat Lt function form Lt(t,pars) computes temporal fluctuations","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Lpar_trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for trace aquatic mosquito model — make_Lpar_trace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_GeRM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_dde","title":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_dde","text":"Make inits GeRM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_GeRM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_dde","text":"","code":"make_MYZinits_GeRM_dde(   nPatches,   Upsilon,   MYZopts = list(),   M0 = 5,   G0 = 1,   Y0 = 1,   Z0 = 1 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_GeRM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_dde","text":"nPatches number patches model Upsilon matrix describing survival dispersal EIP MYZopts list values overwrites defaults M0 total mosquito density patch G0 total parous mosquito density patch Y0 infected mosquito density patch Z0 infectious mosquito density patch","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_GeRM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_dde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_GeRM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_ode","title":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_ode","text":"Make inits GeRM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_GeRM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_ode","text":"","code":"make_MYZinits_GeRM_ode(   nPatches,   MYZopts = list(),   M0 = 5,   G0 = 1,   Y0 = 1,   Z0 = 1 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_GeRM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_ode","text":"nPatches number patches model MYZopts list values overwrites defaults M0 total mosquito density patch G0 total parous mosquito density patch Y0 infected mosquito density patch Z0 infectious mosquito density patch","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_GeRM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for GeRM adult mosquito model — make_MYZinits_GeRM_ode","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_RM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for RM adult mosquito model — make_MYZinits_RM_dde","title":"Make inits for RM adult mosquito model — make_MYZinits_RM_dde","text":"Make inits RM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_RM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for RM adult mosquito model — make_MYZinits_RM_dde","text":"","code":"make_MYZinits_RM_dde(   nPatches,   Upsilon,   MYZopts = list(),   M0 = 5,   P0 = 1,   Y0 = 1,   Z0 = 1 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_RM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for RM adult mosquito model — make_MYZinits_RM_dde","text":"nPatches number patches model Upsilon matrix describing survival dispersal EIP MYZopts list values overwrites defaults M0 total mosquito density patch P0 total parous mosquito density patch Y0 infected mosquito density patch Z0 infectious mosquito density patch","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_RM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for RM adult mosquito model — make_MYZinits_RM_dde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_RM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for RM adult mosquito model — make_MYZinits_RM_ode","title":"Make inits for RM adult mosquito model — make_MYZinits_RM_ode","text":"Make inits RM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_RM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for RM adult mosquito model — make_MYZinits_RM_ode","text":"","code":"make_MYZinits_RM_ode(   nPatches,   MYZopts = list(),   M0 = 5,   P0 = 1,   Y0 = 1,   Z0 = 1 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_RM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for RM adult mosquito model — make_MYZinits_RM_ode","text":"nPatches number patches model MYZopts list values overwrites defaults M0 total mosquito density patch P0 total parous mosquito density patch Y0 infected mosquito density patch Z0 infectious mosquito density patch","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_RM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for RM adult mosquito model — make_MYZinits_RM_ode","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for basicM adult mosquito model — make_MYZinits_basicM","title":"Make inits for basicM adult mosquito model — make_MYZinits_basicM","text":"Make inits basicM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for basicM adult mosquito model — make_MYZinits_basicM","text":"","code":"make_MYZinits_basicM(nPatches, MYZopts = list(), M0 = 5, P0 = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for basicM adult mosquito model — make_MYZinits_basicM","text":"nPatches number patches model MYZopts list values overwrites defaults M0 total mosquito density patch P0 total parous mosquito density patch","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZinits_basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for basicM adult mosquito model — make_MYZinits_basicM","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_GeRM.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for GeRM ODE adult mosquito model — make_MYZpar_GeRM","title":"Make parameters for GeRM ODE adult mosquito model — make_MYZpar_GeRM","text":"Make parameters GeRM ODE adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_GeRM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for GeRM ODE adult mosquito model — make_MYZpar_GeRM","text":"","code":"make_MYZpar_GeRM(   nPatches,   MYZopts = list(),   EIPmod,   calK,   g = 1/12,   g_par = list(),   sigma = 1/8,   sigma_par = list(),   f = 0.3,   f_par = list(),   q = 0.95,   q_par = list(),   nu = 1,   nu_par = list(),   eggsPerBatch = 60 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_GeRM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for GeRM ODE adult mosquito model — make_MYZpar_GeRM","text":"nPatches number patches, integer MYZopts list values overwrites defaults EIPmod list defines EIP model calK mosquito dispersal matrix dimensions nPatches nPatches g mosquito mortality rate g_par parameters configure F_g sigma emigration rate sigma_par parameters configure F_sigma f feeding rate f_par parameters configure F_f q human blood fraction q_par parameters configure F_q nu oviposition rate, per mosquito nu_par parameters configure F_nu eggsPerBatch eggs laid per oviposition","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_GeRM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for GeRM ODE adult mosquito model — make_MYZpar_GeRM","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_Gtrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for Gtrace aquatic mosquito model — make_MYZpar_Gtrace","title":"Make parameters for Gtrace aquatic mosquito model — make_MYZpar_Gtrace","text":"Make parameters Gtrace aquatic mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_Gtrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for Gtrace aquatic mosquito model — make_MYZpar_Gtrace","text":"","code":"make_MYZpar_Gtrace(nPatches, MYZopts, Gm = 1, Gf = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_Gtrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for Gtrace aquatic mosquito model — make_MYZpar_Gtrace","text":"nPatches number patches model MYZopts list overwrite defaults Gm vector mean mosquito densities Gf function form Gf(t, pars) computes temporal fluctuations","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for Gtrace aquatic mosquito model — make_MYZpar_Gtrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for RM ODE adult mosquito model — make_MYZpar_RM","title":"Make parameters for RM ODE adult mosquito model — make_MYZpar_RM","text":"Make parameters RM ODE adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for RM ODE adult mosquito model — make_MYZpar_RM","text":"","code":"make_MYZpar_RM(   nPatches,   MYZopts = list(),   EIPmod,   calK,   g = 1/12,   sigma = 1/8,   f = 0.3,   q = 0.95,   nu = 1,   eggsPerBatch = 60 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for RM ODE adult mosquito model — make_MYZpar_RM","text":"nPatches number patches, integer MYZopts list values overwrites defaults EIPmod list defines EIP model calK mosquito dispersal matrix dimensions nPatches nPatches g mosquito mortality rate sigma emigration rate f feeding rate q human blood fraction nu oviposition rate, per mosquito eggsPerBatch eggs laid per oviposition","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_RM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for RM ODE adult mosquito model — make_MYZpar_RM","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for Ztrace aquatic mosquito model — make_MYZpar_Ztrace","title":"Make parameters for Ztrace aquatic mosquito model — make_MYZpar_Ztrace","text":"Make parameters Ztrace aquatic mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for Ztrace aquatic mosquito model — make_MYZpar_Ztrace","text":"","code":"make_MYZpar_Ztrace(nPatches, MYZopts, f = 0.3, q = 0.95, Zm = 1, Zf = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for Ztrace aquatic mosquito model — make_MYZpar_Ztrace","text":"nPatches integer MYZopts list values overwrites defaults f blood feeding rate q human fraction Zm vector mean mosquito densities Zf function form Zf(t, pars) computes temporal fluctuations","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for Ztrace aquatic mosquito model — make_MYZpar_Ztrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for basicM ODE adult mosquito model — make_MYZpar_basicM","title":"Make parameters for basicM ODE adult mosquito model — make_MYZpar_basicM","text":"Make parameters basicM ODE adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for basicM ODE adult mosquito model — make_MYZpar_basicM","text":"","code":"make_MYZpar_basicM(   nPatches,   MYZopts = list(),   calK,   g = 1/12,   sigma = 1/8,   f = 0.3,   q = 0.95,   nu = 1,   eggsPerBatch = 60 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for basicM ODE adult mosquito model — make_MYZpar_basicM","text":"nPatches number patches MYZopts list values overwrites defaults calK mosquito dispersal matrix dimensions nPatches nPatches g mosquito mortality rate sigma emigration rate f blood feeding rate q human blood feeding fraction nu oviposition rate, per mosquito eggsPerBatch eggs laid per oviposition","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_MYZpar_basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for basicM ODE adult mosquito model — make_MYZpar_basicM","text":"list configured MYZpar","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Omega.html","id":null,"dir":"Reference","previous_headings":"","what":"Make the mosquito demography matrix — make_Omega","title":"Make the mosquito demography matrix — make_Omega","text":"Make mosquito demography matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Omega.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make the mosquito demography matrix — make_Omega","text":"","code":"make_Omega(g, sigma, K, nPatches)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Omega.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make the mosquito demography matrix — make_Omega","text":"g mortality rate sigma emigration  rate K mosquito dispersal matrix nPatches number patches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Omega.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make the mosquito demography matrix — make_Omega","text":"matrix dimensions nPatches nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TaR.html","id":null,"dir":"Reference","previous_headings":"","what":"Make TaR — make_TaR","title":"Make TaR — make_TaR","text":"Make time risk matrix (TaR) time spent matrix circadian function","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TaR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make TaR — make_TaR","text":"","code":"make_TaR(t, pars, i, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_TaR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make TaR — make_TaR","text":"t time pars list host species index s vector species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TaR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make TaR — make_TaR","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.as_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Pass a pre-configured TimeSpent — make_TimeSpent.as_matrix","title":"Pass a pre-configured TimeSpent — make_TimeSpent.as_matrix","text":"Implements make_TimeSpent as_matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.as_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pass a pre-configured TimeSpent — make_TimeSpent.as_matrix","text":"","code":"# S3 method for as_matrix make_TimeSpent(pars, i, TimeSpent, opts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.as_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pass a pre-configured TimeSpent — make_TimeSpent.as_matrix","text":"pars list host species index TimeSpent matrix; string opts list options configure TimeSpent","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.as_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pass a pre-configured TimeSpent — make_TimeSpent.as_matrix","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.athome.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a mosquito dispersal matrix, called TimeSpent with a here / away — make_TimeSpent.athome","title":"Make a mosquito dispersal matrix, called TimeSpent with a here / away — make_TimeSpent.athome","text":"Implements make_TimeSpent as_matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.athome.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a mosquito dispersal matrix, called TimeSpent with a here / away — make_TimeSpent.athome","text":"","code":"# S3 method for athome make_TimeSpent(pars, i, TimeSpent = \"athome\", opts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.athome.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a mosquito dispersal matrix, called TimeSpent with a here / away — make_TimeSpent.athome","text":"pars list host species index TimeSpent matrix; string opts list options configure TimeSpent","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.athome.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a mosquito dispersal matrix, called TimeSpent with a here / away — make_TimeSpent.athome","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a time spent matrix, called TimeSpent — make_TimeSpent","title":"Make a time spent matrix, called TimeSpent — make_TimeSpent","text":"Make time spent matrix, called TimeSpent","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a time spent matrix, called TimeSpent — make_TimeSpent","text":"","code":"make_TimeSpent(pars, i, TimeSpent, opts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a time spent matrix, called TimeSpent — make_TimeSpent","text":"pars list host species index TimeSpent matrix; string opts list options configure TimeSpent","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a time spent matrix, called TimeSpent — make_TimeSpent","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.xy.html","id":null,"dir":"Reference","previous_headings":"","what":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_TimeSpent.xy","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_TimeSpent.xy","text":"Implements make_TimeSpent kernels","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.xy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_TimeSpent.xy","text":"","code":"# S3 method for xy make_TimeSpent(pars, i, TimeSpent = \"xy\", opts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.xy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_TimeSpent.xy","text":"pars list host species index TimeSpent matrix; string opts list options configure TimeSpent","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent.xy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_TimeSpent.xy","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent_athome.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_athome","title":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_athome","text":"Make mosquito dispersal matrix, called TimeSpent","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent_athome.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_athome","text":"","code":"make_TimeSpent_athome(   nPatches,   residence,   opts = list(),   atHome = 1,   travel = 0 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent_athome.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_athome","text":"nPatches number patches residence home patch stratum opts set options overwrites defaults atHome fraction time spent home travel fraction time spent traveling","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent_athome.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_athome","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent_xy.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_xy","title":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_xy","text":"Make mosquito dispersal matrix, called TimeSpent","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent_xy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_xy","text":"","code":"make_TimeSpent_xy(xy, residence, kern, stay, travel)"},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent_xy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_xy","text":"xy xy-locations patches residence home patch stratum kern function gives weight distance stay fraction time spent home travel fraction time spent traveling","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_TimeSpent_xy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a mosquito dispersal matrix, called TimeSpent — make_TimeSpent_xy","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Make initial values for the SIP human model, with defaults — make_Xinits_SIP","title":"Make initial values for the SIP human model, with defaults — make_Xinits_SIP","text":"Make initial values SIP human model, defaults","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make initial values for the SIP human model, with defaults — make_Xinits_SIP","text":"","code":"make_Xinits_SIP(nStrata, Xopts = list(), H0 = NULL, S0 = NULL, I0 = 1, P0 = 0)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make initial values for the SIP human model, with defaults — make_Xinits_SIP","text":"nStrata number population strata Xopts list overwrite defaults H0 initial human population density S0 initial values parameter S I0 initial values parameter P0 initial values parameter P","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make initial values for the SIP human model, with defaults — make_Xinits_SIP","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Make initial values for the SIS human model, with defaults — make_Xinits_SIS","title":"Make initial values for the SIS human model, with defaults — make_Xinits_SIS","text":"Make initial values SIS human model, defaults","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make initial values for the SIS human model, with defaults — make_Xinits_SIS","text":"","code":"make_Xinits_SIS(nStrata, Xopts = list(), H0 = NULL, S0 = NULL, I0 = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make initial values for the SIS human model, with defaults — make_Xinits_SIS","text":"nStrata number strata model Xopts list overwrite defaults H0 initial human population density S0 initial values parameter S I0 initial values parameter ","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make initial values for the SIS human model, with defaults — make_Xinits_SIS","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for hybrid MoI human model — make_Xinits_hMoI","title":"Make inits for hybrid MoI human model — make_Xinits_hMoI","text":"MoI stands Multiplicity Infection, refers malarial superinfection.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for hybrid MoI human model — make_Xinits_hMoI","text":"","code":"make_Xinits_hMoI(nStrata, Xopts = list(), m10 = 2, m20 = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for hybrid MoI human model — make_Xinits_hMoI","text":"nStrata number population strata Xopts list overwrites default values m10 mean MoI among inapparent human infections m20 mean MoI among patent human infections","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xinits_hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for hybrid MoI human model — make_Xinits_hMoI","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for SIP human model, with defaults — make_Xpar_SIP","title":"Make parameters for SIP human model, with defaults — make_Xpar_SIP","text":"Make parameters SIP human model, defaults","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for SIP human model, with defaults — make_Xpar_SIP","text":"","code":"make_Xpar_SIP(   nStrata,   Xopts = list(),   b = 0.55,   r = 1/180,   c = 0.15,   rho = 0.1,   eta = 1/25,   xi = 1/365 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for SIP human model, with defaults — make_Xpar_SIP","text":"nStrata number population strata Xopts list overwrite defaults b transmission probability (efficiency) mosquito human r recovery rate c transmission probability (efficiency) human mosquito rho probability successful treatment upon infection eta prophylaxis waning rate xi background treatment rate","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for SIP human model, with defaults — make_Xpar_SIP","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for SIS human model, with defaults — make_Xpar_SIS","title":"Make parameters for SIS human model, with defaults — make_Xpar_SIS","text":"Make parameters SIS human model, defaults","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for SIS human model, with defaults — make_Xpar_SIS","text":"","code":"make_Xpar_SIS(nStrata, Xopts = list(), b = 0.55, r = 1/180, c = 0.15)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for SIS human model, with defaults — make_Xpar_SIS","text":"nStrata number population strata Xopts list overwrite defaults b transmission probability (efficiency) mosquito human r recovery rate c transmission probability (efficiency) human mosquito","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for SIS human model, with defaults — make_Xpar_SIS","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for hybrid MoI human model — make_Xpar_hMoI","title":"Make parameters for hybrid MoI human model — make_Xpar_hMoI","text":"MoI stands Multiplicity Infection, refers malarial superinfection.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for hybrid MoI human model — make_Xpar_hMoI","text":"","code":"make_Xpar_hMoI(   nStrata,   Xopts = list(),   b = 0.55,   r1 = 1/180,   r2 = 1/70,   c1 = 0.015,   c2 = 0.15 )"},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for hybrid MoI human model — make_Xpar_hMoI","text":"nStrata number human population strata Xopts list overwrites default values b transmission probability (efficiency) mosquito human r1 recovery rate inapparent infections r2 recovery rate patent infections c1 transmission probability (efficiency) inapparent human infections mosquito c2 transmission probability (efficiency) patent human infections mosquito","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for hybrid MoI human model — make_Xpar_hMoI","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for human null model — make_Xpar_trace","title":"Make parameters for human null model — make_Xpar_trace","text":"Make parameters human null model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for human null model — make_Xpar_trace","text":"","code":"make_Xpar_trace(nPatches, Xopts = list(), kappa = 0.1, Kf = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for human null model — make_Xpar_trace","text":"nPatches number patches model Xopts list overwrite defaults kappa value Kf function","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_Xpar_trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for human null model — make_Xpar_trace","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.as_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Pass a pre-configured calK — make_calK.as_matrix","title":"Pass a pre-configured calK — make_calK.as_matrix","text":"Implements make_calK as_matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.as_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pass a pre-configured calK — make_calK.as_matrix","text":"","code":"# S3 method for as_matrix make_calK(nPatches, calK, opts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.as_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pass a pre-configured calK — make_calK.as_matrix","text":"nPatches number patches calK matrix string opts list options configure calK","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.as_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pass a pre-configured calK — make_calK.as_matrix","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.herethere.html","id":null,"dir":"Reference","previous_headings":"","what":"Dispersal to every other patch, with equal probability — make_calK.herethere","title":"Dispersal to every other patch, with equal probability — make_calK.herethere","text":"Implements make_calK herethere model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.herethere.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dispersal to every other patch, with equal probability — make_calK.herethere","text":"","code":"# S3 method for herethere make_calK(nPatches, calK = \"herethere\", opts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.herethere.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dispersal to every other patch, with equal probability — make_calK.herethere","text":"nPatches number patches calK matrix string opts list options configure calK","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.herethere.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Dispersal to every other patch, with equal probability — make_calK.herethere","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a mosquito dispersal matrix, called calK — make_calK","title":"Make a mosquito dispersal matrix, called calK — make_calK","text":"Make mosquito dispersal matrix, called calK","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a mosquito dispersal matrix, called calK — make_calK","text":"","code":"make_calK(nPatches, calK, opts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a mosquito dispersal matrix, called calK — make_calK","text":"nPatches number patches calK matrix string opts list options configure calK","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make a mosquito dispersal matrix, called calK — make_calK","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.xy.html","id":null,"dir":"Reference","previous_headings":"","what":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK.xy","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK.xy","text":"Implements make_calK kernels","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.xy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK.xy","text":"","code":"# S3 method for xy make_calK(nPatches, calK = \"xy\", opts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.xy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK.xy","text":"nPatches number patches calK matrix string opts list options configure calK","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK.xy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK.xy","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK_xy.html","id":null,"dir":"Reference","previous_headings":"","what":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK_xy","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK_xy","text":"Develop mosquito dispersal matrix kernel xy-coordinates","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calK_xy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK_xy","text":"","code":"make_calK_xy(xy, ker)"},{"path":"https://dd-harp.github.io/exDE/reference/make_calK_xy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Develop a mosquito dispersal matrix from a kernel and xy-coordinates — make_calK_xy","text":"xy vector xy-coordinates patch locations ker function weights putative locations distance","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calN.html","id":null,"dir":"Reference","previous_headings":"","what":"Make the habitat membership matrix, calN — make_calN","title":"Make the habitat membership matrix, calN — make_calN","text":"Make habitat membership matrix, calN","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calN.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make the habitat membership matrix, calN — make_calN","text":"","code":"make_calN(nPatches, membership)"},{"path":"https://dd-harp.github.io/exDE/reference/make_calN.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make the habitat membership matrix, calN — make_calN","text":"nPatches number patches membership vector describing patch habitat found","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calN.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make the habitat membership matrix, calN — make_calN","text":"matrix dimensions nPatches nHabitats","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calU.html","id":null,"dir":"Reference","previous_headings":"","what":"Make the egg distribution matrix, calU — make_calU","title":"Make the egg distribution matrix, calU — make_calU","text":"Make egg distribution matrix, calU","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calU.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make the egg distribution matrix, calU — make_calU","text":"","code":"make_calU(calN, searchWts = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/make_calU.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make the egg distribution matrix, calU — make_calU","text":"calN habitat membership matrix searchWts habitat search weights","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calU.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make the egg distribution matrix, calU — make_calU","text":"matrix dimensions nHabitats nPatches","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calU_s.html","id":null,"dir":"Reference","previous_headings":"","what":"Make the egg distribution matrix, calU — make_calU_s","title":"Make the egg distribution matrix, calU — make_calU_s","text":"Make egg distribution matrix, calU","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calU_s.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make the egg distribution matrix, calU — make_calU_s","text":"","code":"make_calU_s(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_calU_s.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make the egg distribution matrix, calU — make_calU_s","text":"pars model object s vector species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_calU_s.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make the egg distribution matrix, calU — make_calU_s","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices.html","id":null,"dir":"Reference","previous_headings":"","what":"Set indices for generalized spatial model — make_indices","title":"Set indices for generalized spatial model — make_indices","text":"Set indices generalized spatial model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set indices for generalized spatial model — make_indices","text":"","code":"make_indices(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set indices for generalized spatial model — make_indices","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set indices for generalized spatial model — make_indices","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.basic","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.basic","text":"Implements make_indices_L basic competition model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.basic","text":"","code":"# S3 method for basic make_indices_L(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.basic","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.basic","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L","text":"method dispatches type pars$Lpar. Adds field L_ix parameter list.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L","text":"","code":"make_indices_L(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.trace","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.trace","text":"Implements make_indices_L trace (forced emergence) model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.trace","text":"","code":"# S3 method for trace make_indices_L(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.trace","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_L.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_L.trace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.GeRM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_dde","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_dde","text":"Implements make_indices_MYZ GeRM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.GeRM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_dde","text":"","code":"# S3 method for GeRM_dde make_indices_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.GeRM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_dde","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.GeRM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_dde","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.GeRM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_ode","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_ode","text":"Implements make_indices_MYZ GeRM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.GeRM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_ode","text":"","code":"# S3 method for GeRM_ode make_indices_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.GeRM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_ode","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.GeRM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.GeRM_ode","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.Gtrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_MYZ.Gtrace","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_MYZ.Gtrace","text":"Implements make_indices_MYZ Gtrace (forced emergence) 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make_indices_MYZ.Gtrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.RM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RM_dde","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RM_dde","text":"Implements make_indices_MYZ RM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.RM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RM_dde","text":"","code":"# S3 method for RM_dde make_indices_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.RM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RM_dde","text":"pars list s species 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s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.RM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RM_ode","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.RM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.RM_ode","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_MYZ.Ztrace","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_MYZ.Ztrace","text":"Implements make_indices_MYZ Ztrace (forced emergence) model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_MYZ.Ztrace","text":"","code":"# S3 method for Ztrace make_indices_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_MYZ.Ztrace","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for aquatic stage mosquitoes to parameter list — make_indices_MYZ.Ztrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.basicM","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.basicM","text":"Implements make_indices_MYZ basic M model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.basicM","text":"","code":"# S3 method for basicM make_indices_MYZ(pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ.basicM","text":"pars list s species 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s)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ","text":"pars list s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_MYZ.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for adult mosquitoes to parameter list — make_indices_MYZ","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for human population to parameter list — make_indices_X.SIP","title":"Add indices for human population to parameter list — make_indices_X.SIP","text":"Implements make_indices_X SIP model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for human population to parameter list — make_indices_X.SIP","text":"","code":"# S3 method for SIP make_indices_X(pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for human population to parameter list — make_indices_X.SIP","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for human population to parameter list — make_indices_X.SIP","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for human population to parameter list — make_indices_X.SIS","title":"Add indices for human population to parameter list — make_indices_X.SIS","text":"Implements make_indices_X SIS model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for human population to parameter list — make_indices_X.SIS","text":"","code":"# S3 method for SIS make_indices_X(pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for human population to parameter list — make_indices_X.SIS","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for human population to parameter list — make_indices_X.SIS","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Add indices for human population to parameter list — make_indices_X.hMoI","title":"Add indices for human population to parameter list — make_indices_X.hMoI","text":"Implements make_indices_X hybrid MoI model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for human population to parameter list — make_indices_X.hMoI","text":"","code":"# S3 method for hMoI make_indices_X(pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for human population to parameter list — make_indices_X.hMoI","text":"pars list host species 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model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add indices for human population to parameter list — make_indices_X.trace","text":"","code":"# S3 method for trace make_indices_X(pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add indices for human population to parameter list — make_indices_X.trace","text":"pars list host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_indices_X.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add indices for human population to parameter list — make_indices_X.trace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_inits_L_basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for basic competition aquatic mosquito model — make_inits_L_basic","title":"Make inits for basic competition aquatic mosquito model — make_inits_L_basic","text":"Make inits basic competition aquatic mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_inits_L_basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for basic competition aquatic mosquito model — make_inits_L_basic","text":"","code":"make_inits_L_basic(pars, L0)"},{"path":"https://dd-harp.github.io/exDE/reference/make_inits_L_basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for basic competition aquatic mosquito model — make_inits_L_basic","text":"pars list L0 initial conditions","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_inits_L_basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for basic competition aquatic mosquito model — make_inits_L_basic","text":"list Linits added","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_inits_L_trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for trace aquatic mosquito model — make_inits_L_trace","title":"Make parameters for trace aquatic mosquito model — make_inits_L_trace","text":"Make parameters trace aquatic mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_inits_L_trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for trace aquatic mosquito model — make_inits_L_trace","text":"","code":"make_inits_L_trace(pars, L0 = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/make_inits_L_trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for trace aquatic mosquito model — make_inits_L_trace","text":"pars list L0 set NULL trace 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Upsilon0)"},{"path":"https://dd-harp.github.io/exDE/reference/make_inits_MYZ_GeRM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for GeRM adult mosquito model — make_inits_MYZ_GeRM_dde","text":"pars list M0 total mosquito density patch G0 total parous mosquito density patch Y0 infected mosquito density patch Z0 infectious mosquito density patch Upsilon0 initial values Upsilon","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_inits_MYZ_GeRM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for GeRM adult mosquito model — make_inits_MYZ_GeRM_dde","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_inits_MYZ_GeRM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for GeRM adult mosquito model — make_inits_MYZ_GeRM_ode","title":"Make inits for GeRM adult mosquito model — make_inits_MYZ_GeRM_ode","text":"Make 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model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_inits_MYZ_Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for Gtrace aquatic mosquito model — make_inits_MYZ_Gtrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_inits_MYZ_RM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for RM adult mosquito model — make_inits_MYZ_RM_dde","title":"Make inits for RM adult mosquito model — make_inits_MYZ_RM_dde","text":"Make inits RM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_inits_MYZ_RM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for RM adult mosquito model — make_inits_MYZ_RM_dde","text":"","code":"make_inits_MYZ_RM_dde(pars, M0, P0, Y0, Z0, 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make_parameters_demography_null","text":"pars list H size human population strata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_demography_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for null human demography model — make_parameters_demography_null","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_xde.html","id":null,"dir":"Reference","previous_headings":"","what":"Make base parameters, assuming nVectors = nHosts = 1 — make_parameters_xde","title":"Make base parameters, assuming nVectors = nHosts = 1 — make_parameters_xde","text":"Make base parameters, assuming nVectors = nHosts = 1","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_xde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make base parameters, assuming nVectors = nHosts = 1 — make_parameters_xde","text":"","code":"make_parameters_xde(solve_as = \"dde\")"},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_xde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make base parameters, assuming nVectors = nHosts = 1 — make_parameters_xde","text":"solve_as, either \"ode\" \"dde\"","code":""},{"path":"https://dd-harp.github.io/exDE/reference/make_parameters_xde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make base parameters, assuming nVectors = nHosts = 1 — make_parameters_xde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calD.html","id":null,"dir":"Reference","previous_headings":"","what":"Parasite dispersal by humans — metric_calD","title":"Parasite dispersal by humans — metric_calD","text":"Compute p p matrix \\(\\mathcal{D}\\) whose columns describe potentially infectious person time persons patch dispersed across patches. $$\\mathcal{D} = \\mbox{diag}\\left(W \\right) \\cdot \\beta^T \\cdot \\mbox{diag}\\left(bDH\\right) \\cdot \\beta$$","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calD.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parasite dispersal by humans — metric_calD","text":"","code":"metric_calD(W, beta, b, D, H)"},{"path":"https://dd-harp.github.io/exDE/reference/metric_calD.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parasite dispersal by humans — metric_calD","text":"W ambient human population patch beta biting distribution matrix b transmission efficiency mosquitoes humans D human transmitting capacity H human population size strata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calD.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parasite dispersal by humans — metric_calD","text":"numeric matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calR.html","id":null,"dir":"Reference","previous_headings":"","what":"Parasite Dispersal through one Parasite Generation (Humans) — metric_calR","title":"Parasite Dispersal through one Parasite Generation (Humans) — metric_calR","text":"Computes n n matrix describing parasite dispersal infecteds (columns) infectees (rows). $$\\mathcal{R} =   b \\beta \\cdot {\\cal V}  \\cdot \\mbox{diag}\\left(W \\right) \\cdot \\beta^T  \\cdot \\mbox{diag}\\left(DH\\right)$$","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parasite Dispersal through one Parasite Generation (Humans) — metric_calR","text":"","code":"metric_calR(b, beta, calV, W, D, H)"},{"path":"https://dd-harp.github.io/exDE/reference/metric_calR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parasite Dispersal through one Parasite Generation (Humans) — metric_calR","text":"b transmission efficiency mosquitoes humans beta biting distribution matrix calV parasite dispersal mosquitoes matrix (see metric_calV) W ambient human population patch D human transmitting capacity H human population size strata","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calR.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parasite Dispersal through one Parasite Generation (Humans) — metric_calR","text":"numeric matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calV.html","id":null,"dir":"Reference","previous_headings":"","what":"Parasite dispersal by mosquitoes — metric_calV","title":"Parasite dispersal by mosquitoes — metric_calV","text":"Compute p p matrix \\(\\mathcal{V}\\) whose columns describe infective bites arising mosquitoes biting single human single day dispersed patches, accounting movement mortality. $$\\mathcal{V} = fq\\Omega^{-1} \\cdot e^{-\\Omega\\tau} \\cdot \\mbox{diag}\\left(\\frac{fqM}{W}\\right)$$","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calV.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parasite dispersal by mosquitoes — metric_calV","text":"","code":"metric_calV(f, q, Omega, tau, M, W)"},{"path":"https://dd-harp.github.io/exDE/reference/metric_calV.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parasite dispersal by mosquitoes — metric_calV","text":"f feeding rate q fraction bloodmeals taken humans Omega mosquito demography matrix tau duration extrinsic incubation period M size mosquito population patch W ambient human population patch","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calV.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parasite dispersal by mosquitoes — metric_calV","text":"numeric matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Parasite Dispersal through one Parasite Generation (Mosquitoes) — metric_calZ","title":"Parasite Dispersal through one Parasite Generation (Mosquitoes) — metric_calZ","text":"Computes p p matrix describing parasite dispersal infecteds (columns) infectees (rows). $$\\mathcal{Z} = e^{-\\Omega\\tau} \\cdot \\mbox{diag}\\left( \\frac{fq M}{W} \\right) \\cdot {\\cal D} \\cdot  fq\\Omega^{-1}$$","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parasite Dispersal through one Parasite Generation (Mosquitoes) — metric_calZ","text":"","code":"metric_calZ(Omega, tau, f, q, M, W, calD)"},{"path":"https://dd-harp.github.io/exDE/reference/metric_calZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parasite Dispersal through one Parasite Generation (Mosquitoes) — metric_calZ","text":"Omega mosquito demography matrix tau duration extrinsic incubation period f feeding rate q fraction bloodmeals taken humans M size mosquito population patch W ambient human population patch calD parasite dispersal humans matrix (see metric_calD)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/metric_calZ.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parasite Dispersal through one Parasite Generation (Mosquitoes) — metric_calZ","text":"numeric matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of an object returned by deSolve — parse_deout","title":"Parse the output of an object returned by deSolve — parse_deout","text":"Parse output object returned deSolve","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of an object returned by deSolve — parse_deout","text":"","code":"parse_deout(deout, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of an object returned by deSolve — parse_deout","text":"deout matrix orbits returned deSolve pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of an object returned by deSolve — parse_deout","text":"varslist list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the variable names for the basic model — parse_deout_L.basic","title":"Parse the variable names for the basic model — parse_deout_L.basic","text":"Implements parse_deout_L basic competition model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the variable names for the basic model — parse_deout_L.basic","text":"","code":"# S3 method for basic parse_deout_L(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the variable names for the basic model — parse_deout_L.basic","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the variable names for the basic model — parse_deout_L.basic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return the variables by name in a list — parse_deout_L","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_L","text":"method dispatches type pars$Lpar. Attaches state variables aquatic ecology model list returns ","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_L","text":"","code":"parse_deout_L(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_L","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the variable names for the trace model — parse_deout_L.trace","title":"Parse the variable names for the trace model — parse_deout_L.trace","text":"Implements parse_deout_L trace model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the variable names for the trace model — parse_deout_L.trace","text":"","code":"# S3 method for trace parse_deout_L(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the variable names for the trace model — parse_deout_L.trace","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_L.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the variable names for the trace model — parse_deout_L.trace","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.GeRM.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the GeRM model — parse_deout_MYZ.GeRM","title":"Parse the output of deSolve and return variables for the GeRM model — parse_deout_MYZ.GeRM","text":"Implements parse_deout_MYZ GeRM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.GeRM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the GeRM model — parse_deout_MYZ.GeRM","text":"","code":"# S3 method for GeRM parse_deout_MYZ(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.GeRM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the GeRM model — parse_deout_MYZ.GeRM","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.GeRM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the GeRM model — parse_deout_MYZ.GeRM","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.Gtrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the Gtrace model — parse_deout_MYZ.Gtrace","title":"Parse the output of deSolve and return variables for the Gtrace model — parse_deout_MYZ.Gtrace","text":"Implements parse_deout_MYZ Gtrace","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.Gtrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the Gtrace model — parse_deout_MYZ.Gtrace","text":"","code":"# S3 method for Gtrace parse_deout_MYZ(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.Gtrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the Gtrace model — parse_deout_MYZ.Gtrace","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the Gtrace model — parse_deout_MYZ.Gtrace","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the RM model — parse_deout_MYZ.RM","title":"Parse the output of deSolve and return variables for the RM model — parse_deout_MYZ.RM","text":"Implements parse_deout_MYZ RM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the RM model — parse_deout_MYZ.RM","text":"","code":"# S3 method for RM parse_deout_MYZ(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the RM model — parse_deout_MYZ.RM","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.RM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the RM model — parse_deout_MYZ.RM","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the Ztrace model — parse_deout_MYZ.Ztrace","title":"Parse the output of deSolve and return variables for the Ztrace model — parse_deout_MYZ.Ztrace","text":"Implements parse_deout_MYZ Ztrace","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the Ztrace model — parse_deout_MYZ.Ztrace","text":"","code":"# S3 method for Ztrace parse_deout_MYZ(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the Ztrace model — parse_deout_MYZ.Ztrace","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the Ztrace model — parse_deout_MYZ.Ztrace","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the basicM model — parse_deout_MYZ.basicM","title":"Parse the output of deSolve and return variables for the basicM model — parse_deout_MYZ.basicM","text":"Implements parse_deout_MYZ basicM model.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the basicM model — parse_deout_MYZ.basicM","text":"","code":"# S3 method for basicM parse_deout_MYZ(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the basicM model — parse_deout_MYZ.basicM","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the basicM model — parse_deout_MYZ.basicM","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return the variables by name in a list — parse_deout_MYZ","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_MYZ","text":"method dispatches type pars$MYZpar. computes variables name returns named list.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_MYZ","text":"","code":"parse_deout_MYZ(deout, pars, s)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_MYZ","text":"deout matrix outputs deSolve pars list defines model s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_MYZ.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_MYZ","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the SIP model — parse_deout_X.SIP","title":"Parse the output of deSolve and return variables for the SIP model — parse_deout_X.SIP","text":"Implements parse_deout_X SIP model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the SIP model — parse_deout_X.SIP","text":"","code":"# S3 method for SIP parse_deout_X(deout, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the SIP model — parse_deout_X.SIP","text":"deout matrix outputs deSolve pars list defines model host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the SIP model — parse_deout_X.SIP","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the SIS model — parse_deout_X.SIS","title":"Parse the output of deSolve and return variables for the SIS model — parse_deout_X.SIS","text":"Implements parse_deout_X SIS model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the SIS model — parse_deout_X.SIS","text":"","code":"# S3 method for SIS parse_deout_X(deout, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the SIS model — parse_deout_X.SIS","text":"deout matrix outputs deSolve pars list defines model host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the SIS model — parse_deout_X.SIS","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the hMoI model — parse_deout_X.hMoI","title":"Parse the output of deSolve and return variables for the hMoI model — parse_deout_X.hMoI","text":"Implements parse_deout_X hMoI model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the hMoI model — parse_deout_X.hMoI","text":"","code":"# S3 method for hMoI parse_deout_X(deout, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the hMoI model — parse_deout_X.hMoI","text":"deout matrix outputs deSolve pars list defines model host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the hMoI model — parse_deout_X.hMoI","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return the variables by name in a list — parse_deout_X","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_X","text":"method dispatches type pars$Xpar. Adds variables X model list returns ","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_X","text":"","code":"parse_deout_X(deout, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return the variables by name in a list — parse_deout_X","text":"deout matrix outputs deSolve pars list defines model host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of deSolve and return variables for the trace model — parse_deout_X.trace","title":"Parse the output of deSolve and return variables for the trace model — parse_deout_X.trace","text":"Implements parse_deout_X trace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of deSolve and return variables for the trace model — parse_deout_X.trace","text":"","code":"# S3 method for trace parse_deout_X(deout, pars, i)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of deSolve and return variables for the trace model — parse_deout_X.trace","text":"deout matrix outputs deSolve pars list defines model host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_X.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of deSolve and return variables for the trace model — parse_deout_X.trace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_vec.html","id":null,"dir":"Reference","previous_headings":"","what":"Parse the output of an object returned by deSolve — parse_deout_vec","title":"Parse the output of an object returned by deSolve — parse_deout_vec","text":"Parse output object returned deSolve","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_vec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Parse the output of an object returned by deSolve — parse_deout_vec","text":"","code":"parse_deout_vec(vec, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_vec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Parse the output of an object returned by deSolve — parse_deout_vec","text":"vec vector variables, returned rootsolve pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/parse_deout_vec.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Parse the output of an object returned by deSolve — parse_deout_vec","text":"varslist list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_BFpar_static.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the blood feeding model — setup_BFpar_static","title":"Set up the blood feeding model — setup_BFpar_static","text":"sets list stores information required blood feeding model, including information humans (residence vector, search weights blood feeding mosquitoes); mosquitoes circadian pattern (F_circadian); derived structures, including time spent (TimeSpent) time risk (TaR) matrices. also sets objects required blood feeding, including host availability species (Wi) hosts (W), blood hosts (), total blood availability (B). Finally, sets lists hold mixing matrix (beta), transmission terms describing entomological inoculation rate (EIR eir), force infection (FoI), net infectiousness (kappa ni).","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_BFpar_static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the blood feeding model — setup_BFpar_static","text":"","code":"setup_BFpar_static(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_BFpar_static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the blood feeding model — setup_BFpar_static","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_BFpar_static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the blood feeding model — setup_BFpar_static","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_BloodFeeding.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up blood feeding — setup_BloodFeeding","title":"Set up blood feeding — setup_BloodFeeding","text":"sets list stores information","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_BloodFeeding.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up blood feeding — setup_BloodFeeding","text":"","code":"setup_BloodFeeding(   pars,   i,   s = 1,   BFopts = list(),   residence = 1,   searchWts = 1,   F_circadian = NULL )"},{"path":"https://dd-harp.github.io/exDE/reference/setup_BloodFeeding.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up blood feeding — setup_BloodFeeding","text":"pars list host species index s vector species index BFopts list residence patch stratum resides searchWts blood feeding search weight stratum F_circadian function computes relative mosquito blood feeding activity rates time day","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_BloodFeeding.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up blood feeding — setup_BloodFeeding","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EGGpar_static.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the structures required for egg laying — setup_EGGpar_static","title":"Setup the structures required for egg laying — setup_EGGpar_static","text":"sets object EGGpar, holds information egg laying model. Several terms expected differ vector species, including search weights (searchWts), fraction eggs laid habitat sometimes suitable (Qfrac), egg deposition matrix (calU), habitat egg laying rate (eggs_laid). function sets lists.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EGGpar_static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the structures required for egg laying — setup_EGGpar_static","text":"","code":"setup_EGGpar_static(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_EGGpar_static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the structures required for egg laying — setup_EGGpar_static","text":"pars model object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EGGpar_static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the structures required for egg laying — setup_EGGpar_static","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the static model for control forcing (do nothing) — setup_EIP","title":"Set up the static model for control forcing (do nothing) — setup_EIP","text":"Set static model control forcing (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the static model for control forcing (do nothing) — setup_EIP","text":"","code":"setup_EIP(EIPname = \"static\", EIPopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_EIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the static model for control forcing (do nothing) — setup_EIP","text":"EIPname class name function EIPopts list overwrites default options","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the static model for control forcing (do nothing) — setup_EIP","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EIP.static.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up a static model for the EIP — setup_EIP.static","title":"Set up a static model for the EIP — setup_EIP.static","text":"Set static model EIP","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EIP.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up a static model for the EIP — setup_EIP.static","text":"","code":"# S3 method for static setup_EIP(EIPname, EIPopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_EIP.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up a static model for the EIP — setup_EIP.static","text":"EIPname class name function EIPopts list overwrites default options","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EIP.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up a static model for the EIP — setup_EIP.static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EggLaying_simple.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup egg laying for most models — setup_EggLaying_simple","title":"Setup egg laying for most models — setup_EggLaying_simple","text":"Sets egg-deposition matrix calU s^th species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EggLaying_simple.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup egg laying for most models — setup_EggLaying_simple","text":"","code":"setup_EggLaying_simple(pars, s, searchQ = 1, Lopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_EggLaying_simple.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup egg laying for most models — setup_EggLaying_simple","text":"pars model object s vector species index searchQ membership matrix Lopts list options override defaults","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EggLaying_simple.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup egg laying for most models — setup_EggLaying_simple","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EggLaying_static.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup egg laying for most models — setup_EggLaying_static","title":"Setup egg laying for most models — setup_EggLaying_static","text":"Sets egg-deposition matrix calU s^th species","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EggLaying_static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup egg laying for most models — setup_EggLaying_static","text":"","code":"setup_EggLaying_static(pars, s, searchQ = 1, Lopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_EggLaying_static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup egg laying for most models — setup_EggLaying_static","text":"pars model object s vector species index searchQ membership matrix Lopts list options override defaults","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_EggLaying_static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup egg laying for most models — setup_EggLaying_static","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Hpar_static.html","id":null,"dir":"Reference","previous_headings":"","what":"A utility to set up Hpar — setup_Hpar_static","title":"A utility to set up Hpar — setup_Hpar_static","text":"utility set Hpar","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Hpar_static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A utility to set up Hpar — setup_Hpar_static","text":"","code":"setup_Hpar_static(pars, i, HPop = 1000)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Hpar_static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A utility to set up Hpar — setup_Hpar_static","text":"pars list host species index HPop numeric vector population densities","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Hpar_static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A utility to set up Hpar — setup_Hpar_static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the basic model — setup_Linits.basic","title":"Setup the basic model — setup_Linits.basic","text":"Implements setup_Linits basic model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the basic model — setup_Linits.basic","text":"","code":"# S3 method for basic setup_Linits(pars, s, Lopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the basic model — setup_Linits.basic","text":"pars list s species index Lopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the basic model — setup_Linits.basic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to set up adult mosquito models — setup_Linits","title":"A function to set up adult mosquito models — setup_Linits","text":"method dispatches Lname.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to set up adult mosquito models — setup_Linits","text":"","code":"setup_Linits(pars, s, Lopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to set up adult mosquito models — setup_Linits","text":"pars list s species index Lopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to set up adult mosquito models — setup_Linits","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the trace model — setup_Linits.trace","title":"Setup the trace model — setup_Linits.trace","text":"Implements setup_Linits trace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the trace model — setup_Linits.trace","text":"","code":"# S3 method for trace setup_Linits(pars, s, Lopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the trace model — setup_Linits.trace","text":"pars list s species index Lopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Linits.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the trace model — setup_Linits.trace","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Lpar for the basic model — setup_Lpar.basic","title":"Setup Lpar for the basic model — setup_Lpar.basic","text":"Implements setup_Lpar basic model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Lpar for the basic model — setup_Lpar.basic","text":"","code":"# S3 method for basic setup_Lpar(Lname, pars, s, Lopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Lpar for the basic model — setup_Lpar.basic","text":"Lname class name aquatic model pars list s species index Lopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Lpar for the basic model — setup_Lpar.basic","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to set up adult mosquito models — setup_Lpar","title":"A function to set up adult mosquito models — setup_Lpar","text":"method dispatches Lname.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to set up adult mosquito models — setup_Lpar","text":"","code":"setup_Lpar(Lname, pars, s, Lopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to set up adult mosquito models — setup_Lpar","text":"Lname class name aquatic model pars list s species index Lopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to set up adult mosquito models — setup_Lpar","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Lpar for the trace model — setup_Lpar.trace","title":"Setup Lpar for the trace model — setup_Lpar.trace","text":"Implements setup_Lpar trace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Lpar for the trace model — setup_Lpar.trace","text":"","code":"# S3 method for trace setup_Lpar(Lname, pars, s, Lopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Lpar for the trace model — setup_Lpar.trace","text":"Lname class name aquatic model pars list s species index Lopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Lpar.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Lpar for the trace model — setup_Lpar.trace","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.GeRM.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the GeRM model — setup_MYZinits.GeRM","title":"Setup the GeRM model — setup_MYZinits.GeRM","text":"Implements setup_MYZinits GeRM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.GeRM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the GeRM model — setup_MYZinits.GeRM","text":"","code":"# S3 method for GeRM setup_MYZinits(pars, s, MYZopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.GeRM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the GeRM model — setup_MYZinits.GeRM","text":"pars list s species index MYZopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.GeRM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the GeRM model — setup_MYZinits.GeRM","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.Gtrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the Gtrace model — setup_MYZinits.Gtrace","title":"Setup the Gtrace model — setup_MYZinits.Gtrace","text":"Implements setup_MYZinits Gtrace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.Gtrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the Gtrace model — setup_MYZinits.Gtrace","text":"","code":"# S3 method for Gtrace setup_MYZinits(pars, s, MYZopts = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.Gtrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the Gtrace model — setup_MYZinits.Gtrace","text":"pars list s species index MYZopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the Gtrace model — setup_MYZinits.Gtrace","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup initial values for the RM model — setup_MYZinits.RM","title":"Setup initial values for the RM model — setup_MYZinits.RM","text":"Implements setup_MYZinits RM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup initial values for the RM model — setup_MYZinits.RM","text":"","code":"# S3 method for RM setup_MYZinits(pars, s, MYZopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup initial values for the RM model — setup_MYZinits.RM","text":"pars list s species index MYZopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.RM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup initial values for the RM model — setup_MYZinits.RM","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the Ztrace model — setup_MYZinits.Ztrace","title":"Setup the Ztrace model — setup_MYZinits.Ztrace","text":"Implements setup_MYZinits Ztrace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the Ztrace model — setup_MYZinits.Ztrace","text":"","code":"# S3 method for Ztrace setup_MYZinits(pars, s, MYZopts = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the Ztrace model — setup_MYZinits.Ztrace","text":"pars list s species index MYZopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the Ztrace model — setup_MYZinits.Ztrace","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the basicM model — setup_MYZinits.basicM","title":"Setup the basicM model — setup_MYZinits.basicM","text":"Implements setup_MYZinits basicM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the basicM model — setup_MYZinits.basicM","text":"","code":"# S3 method for basicM setup_MYZinits(pars, s, MYZopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the basicM model — setup_MYZinits.basicM","text":"pars list s species index MYZopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the basicM model — setup_MYZinits.basicM","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to set up adult mosquito models — setup_MYZinits","title":"A function to set up adult mosquito models — setup_MYZinits","text":"method dispatches MYZname.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to set up adult mosquito models — setup_MYZinits","text":"","code":"setup_MYZinits(pars, s, MYZopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to set up adult mosquito models — setup_MYZinits","text":"pars list s species index MYZopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZinits.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to set up adult mosquito models — setup_MYZinits","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.GeRM.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup MYZpar for the GeRM model — setup_MYZpar.GeRM","title":"Setup MYZpar for the GeRM model — setup_MYZpar.GeRM","text":"Implements setup_MYZpar GeRM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.GeRM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup MYZpar for the GeRM model — setup_MYZpar.GeRM","text":"","code":"# S3 method for GeRM setup_MYZpar(MYZname, pars, s, MYZopts = list(), EIPmod, calK)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.GeRM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup MYZpar for the GeRM model — setup_MYZpar.GeRM","text":"MYZname name model pars list s species index MYZopts list EIPmod list calK matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.GeRM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup MYZpar for the GeRM model — setup_MYZpar.GeRM","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.Gtrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the Gtrace — setup_MYZpar.Gtrace","title":"Setup the Gtrace — setup_MYZpar.Gtrace","text":"Implements setup_MYZpar Gtrace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.Gtrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the Gtrace — setup_MYZpar.Gtrace","text":"","code":"# S3 method for Gtrace setup_MYZpar(MYZname, pars, s, MYZopts = NULL, EIPmod = NULL, calK = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.Gtrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the Gtrace — setup_MYZpar.Gtrace","text":"MYZname name model pars list s species index MYZopts list EIPmod list calK matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the Gtrace — setup_MYZpar.Gtrace","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.RM.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup MYZpar for the RM model — setup_MYZpar.RM","title":"Setup MYZpar for the RM model — setup_MYZpar.RM","text":"Implements setup_MYZpar RM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.RM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup MYZpar for the RM model — setup_MYZpar.RM","text":"","code":"# S3 method for RM setup_MYZpar(MYZname, pars, s, MYZopts = list(), EIPmod, calK)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.RM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup MYZpar for the RM model — setup_MYZpar.RM","text":"MYZname name model pars list s species index MYZopts list EIPmod list calK matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.RM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup MYZpar for the RM model — setup_MYZpar.RM","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup the Ztrace model — setup_MYZpar.Ztrace","title":"Setup the Ztrace model — setup_MYZpar.Ztrace","text":"Implements setup_MYZpar Ztrace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup the Ztrace model — setup_MYZpar.Ztrace","text":"","code":"# S3 method for Ztrace setup_MYZpar(MYZname, pars, s, MYZopts = NULL, EIPmod = NULL, calK = NULL)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup the Ztrace model — setup_MYZpar.Ztrace","text":"MYZname name model pars list s species index MYZopts list EIPmod list calK matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup the Ztrace model — setup_MYZpar.Ztrace","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup MYZpar for the basicM model — setup_MYZpar.basicM","title":"Setup MYZpar for the basicM model — setup_MYZpar.basicM","text":"Implements setup_MYZpar basicM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup MYZpar for the basicM model — setup_MYZpar.basicM","text":"","code":"# S3 method for basicM setup_MYZpar(MYZname, pars, s, MYZopts = list(), EIPmod = NULL, calK)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup MYZpar for the basicM model — setup_MYZpar.basicM","text":"MYZname name model pars list s species index MYZopts list EIPmod list calK matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup MYZpar for the basicM model — setup_MYZpar.basicM","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to set up adult mosquito models — setup_MYZpar","title":"A function to set up adult mosquito models — setup_MYZpar","text":"method dispatches MYZname.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to set up adult mosquito models — setup_MYZpar","text":"","code":"setup_MYZpar(   MYZname,   pars,   s,   MYZopts = list(),   EIPmod = setup_eip_static(),   calK = diag(1) )"},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to set up adult mosquito models — setup_MYZpar","text":"MYZname name model pars list s species index MYZopts list EIPmod list calK matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_MYZpar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to set up adult mosquito models — setup_MYZpar","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xinits.SIP — setup_Xinits.SIP","title":"Setup Xinits.SIP — setup_Xinits.SIP","text":"Implements setup_Xinits SIP model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xinits.SIP — setup_Xinits.SIP","text":"","code":"# S3 method for SIP setup_Xinits(pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xinits.SIP — setup_Xinits.SIP","text":"pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xinits.SIP — setup_Xinits.SIP","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xinits.SIS — setup_Xinits.SIS","title":"Setup Xinits.SIS — setup_Xinits.SIS","text":"Implements setup_Xinits SIS model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xinits.SIS — setup_Xinits.SIS","text":"","code":"# S3 method for SIS setup_Xinits(pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xinits.SIS — setup_Xinits.SIS","text":"pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xinits.SIS — setup_Xinits.SIS","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xinits.hMoI — setup_Xinits.hMoI","title":"Setup Xinits.hMoI — setup_Xinits.hMoI","text":"Implements setup_Xinits hMoI model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xinits.hMoI — setup_Xinits.hMoI","text":"","code":"# S3 method for hMoI setup_Xinits(pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xinits.hMoI — setup_Xinits.hMoI","text":"pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xinits.hMoI — setup_Xinits.hMoI","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to set up Xpar — setup_Xinits","title":"A function to set up Xpar — setup_Xinits","text":"method dispatches Xname.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to set up Xpar — setup_Xinits","text":"","code":"setup_Xinits(pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to set up Xpar — setup_Xinits","text":"pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to set up Xpar — setup_Xinits","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xinits.trace — setup_Xinits.trace","title":"Setup Xinits.trace — setup_Xinits.trace","text":"Implements setup_Xinits trace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xinits.trace — setup_Xinits.trace","text":"","code":"# S3 method for trace setup_Xinits(pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xinits.trace — setup_Xinits.trace","text":"pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xinits.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xinits.trace — setup_Xinits.trace","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xpar.SIP — setup_Xpar.SIP","title":"Setup Xpar.SIP — setup_Xpar.SIP","text":"Implements setup_Xpar SIP model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xpar.SIP — setup_Xpar.SIP","text":"","code":"# S3 method for SIP setup_Xpar(Xname, pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xpar.SIP — setup_Xpar.SIP","text":"Xname character string pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xpar.SIP — setup_Xpar.SIP","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xpar.SIS — setup_Xpar.SIS","title":"Setup Xpar.SIS — setup_Xpar.SIS","text":"Implements setup_Xpar SIS model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xpar.SIS — setup_Xpar.SIS","text":"","code":"# S3 method for SIS setup_Xpar(Xname, pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xpar.SIS — setup_Xpar.SIS","text":"Xname character string pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xpar.SIS — setup_Xpar.SIS","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xpar.hMoI — setup_Xpar.hMoI","title":"Setup Xpar.hMoI — setup_Xpar.hMoI","text":"Implements setup_Xpar hMoI model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xpar.hMoI — setup_Xpar.hMoI","text":"","code":"# S3 method for hMoI setup_Xpar(Xname, pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xpar.hMoI — setup_Xpar.hMoI","text":"Xname character string pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xpar.hMoI — setup_Xpar.hMoI","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to set up Xpar — setup_Xpar","title":"A function to set up Xpar — setup_Xpar","text":"method dispatches Xname.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to set up Xpar — setup_Xpar","text":"","code":"setup_Xpar(Xname, pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A function to set up Xpar — setup_Xpar","text":"Xname character string pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A function to set up Xpar — setup_Xpar","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup Xpar.trace — setup_Xpar.trace","title":"Setup Xpar.trace — setup_Xpar.trace","text":"Implements setup_Xpar trace model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup Xpar.trace — setup_Xpar.trace","text":"","code":"# S3 method for trace setup_Xpar(Xname, pars, i, Xopts = list())"},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup Xpar.trace — setup_Xpar.trace","text":"Xname character string pars list host species index Xopts list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_Xpar.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup Xpar.trace — setup_Xpar.trace","text":"list vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_abiotic_forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for the null model of abiotic forcing (do nothing) — setup_abiotic_forced","title":"Make parameters for the null model of abiotic forcing (do nothing) — setup_abiotic_forced","text":"Make parameters null model abiotic forcing (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_abiotic_forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for the null model of abiotic forcing (do nothing) — setup_abiotic_forced","text":"","code":"setup_abiotic_forced(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_abiotic_forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for the null model of abiotic forcing (do nothing) — setup_abiotic_forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_abiotic_forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for the null model of abiotic forcing (do nothing) — setup_abiotic_forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_abiotic_null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the null model for exogenous forcing (do nothing) — setup_abiotic_null","title":"Set up the null model for exogenous forcing (do nothing) — setup_abiotic_null","text":"Set null model exogenous forcing (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_abiotic_null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the null model for exogenous forcing (do nothing) — setup_abiotic_null","text":"","code":"setup_abiotic_null(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_abiotic_null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the null model for exogenous forcing (do nothing) — setup_abiotic_null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_abiotic_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the null model for exogenous forcing (do nothing) — setup_abiotic_null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_area_spray_null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the null model for area spraying (do nothing) — setup_area_spray_null","title":"Set up the null model for area spraying (do nothing) — setup_area_spray_null","text":"Set null model area spraying (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_area_spray_null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the null model for area spraying (do nothing) — setup_area_spray_null","text":"","code":"setup_area_spray_null(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_area_spray_null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the null model for area spraying (do nothing) — setup_area_spray_null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_area_spray_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the null model for area spraying (do nothing) — setup_area_spray_null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior.forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup behavior — setup_behavior.forced","title":"Setup behavior — setup_behavior.forced","text":"Setup behavior","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior.forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Setup behavior — setup_behavior.forced","text":"","code":"# S3 method for forced setup_behavior(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior.forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Setup behavior — setup_behavior.forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior.forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Setup behavior — setup_behavior.forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_behavior.html","id":null,"dir":"Reference","previous_headings":"","what":"Setup behavior — setup_behavior","title":"Setup behavior — setup_behavior","text":"Setup 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setup_control.null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_control_forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up a model with some control — setup_control_forced","title":"Set up a model with some control — setup_control_forced","text":"Set model control","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_control_forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up a model with some control — setup_control_forced","text":"","code":"setup_control_forced(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_control_forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up a model with some control — setup_control_forced","text":"pars 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(nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_development_null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the null model for developments (do nothing) — setup_development_null","text":"","code":"setup_development_null(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_development_null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the null model for developments (do nothing) — setup_development_null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_development_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the null model for developments (do nothing) — setup_development_null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_eip_static.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up a static model for 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setup_eip_static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_exposure_nb.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for the null model of exposure — setup_exposure_nb","title":"Make parameters for the null model of exposure — setup_exposure_nb","text":"Make parameters null model exposure","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_exposure_nb.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for the null model of exposure — setup_exposure_nb","text":"","code":"setup_exposure_nb(pars, sz)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_exposure_nb.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for the null model of exposure — setup_exposure_nb","text":"pars list sz size parameter, dnbinom(mu=mu, size=size)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_exposure_nb.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for the null model of exposure — setup_exposure_nb","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_exposure_pois.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for the null model of exposure — setup_exposure_pois","title":"Make parameters for the null model of exposure — setup_exposure_pois","text":"Make parameters null model exposure","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_exposure_pois.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for the null model of exposure — 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(nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_sugar_baits_null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the null model for sugar baits (do nothing) — setup_sugar_baits_null","text":"","code":"setup_sugar_baits_null(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_sugar_baits_null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the null model for sugar baits (do nothing) — setup_sugar_baits_null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_sugar_baits_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the null model for sugar baits (do nothing) — setup_sugar_baits_null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_sugar_static.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for the static model for sugar (do nothing) — setup_sugar_static","title":"Make parameters for the static model for sugar (do nothing) — setup_sugar_static","text":"Make parameters static model sugar (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_sugar_static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for the static model for sugar (do nothing) — setup_sugar_static","text":"","code":"setup_sugar_static(pars, Sugar = 0)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_sugar_static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for the static model for sugar (do nothing) — setup_sugar_static","text":"pars list Sugar describes sugar availability","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_sugar_static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for the static 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0.01,   travel_eir_scale = 0,   travel_eir_t = NULL )"},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_eir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up parameters and function for an eir-based travel_malaria model — setup_travel_eir","text":"pars list travel_Opts list, overwrites default values frac_time_spent_traveling fraction time spent travel travel_eir_scale non-negative numeric value scale mean eir experienced traveling travel_eir_t temporal pattern eir experienced traveling","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_eir.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up parameters and function for an eir-based travel_malaria model — setup_travel_eir","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_foi.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up parameters and function for 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FoI","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_foi.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up parameters and function for the FoI-based travel_malaria model — setup_travel_foi","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_static.html","id":null,"dir":"Reference","previous_headings":"","what":"A function to set up malaria importation — setup_travel_static","title":"A function to set up malaria importation — setup_travel_static","text":"Setup static model travel malaria","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_travel_static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A function to set up malaria importation — setup_travel_static","text":"","code":"setup_travel_static(pars, delta = 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setup_vc_null","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_visitors_basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters and functions for the basic model for visitors — setup_visitors_basic","title":"Make parameters and functions for the basic model for visitors — setup_visitors_basic","text":"Make parameters functions basic model visitors","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_visitors_basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters and functions for the basic model for visitors — setup_visitors_basic","text":"","code":"setup_visitors_basic(   pars,   IMopts,   x_scale = 0,   xt = NULL,   V_scale = 0,   Vt = NULL )"},{"path":"https://dd-harp.github.io/exDE/reference/setup_visitors_basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters and functions for the basic model for visitors — setup_visitors_basic","text":"pars list IMopts list x_scale non-negative numeric value set mean x_visitors xt function change pattern x_visitors time V_scale non-negative numeric value set mean availability Visitors Vt function set temporal pattern availability Visitors","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_visitors_basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters and functions for the basic model for visitors — setup_visitors_basic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_visitors_static.html","id":null,"dir":"Reference","previous_headings":"","what":"Make parameters for the static model visitors (no visitors) — setup_visitors_static","title":"Make parameters for the static model visitors (no visitors) — setup_visitors_static","text":"Make parameters static model visitors (visitors)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_visitors_static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make parameters for the static model visitors (no visitors) — setup_visitors_static","text":"","code":"setup_visitors_static(pars, local_frac = 1, Visitors = 0, x_visitors = 0)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_visitors_static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make parameters for the static model visitors (no visitors) — setup_visitors_static","text":"pars list local_frac fraction humans / hosts visitors Visitors availability visitors x_visitors net infectiousness visitors","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_visitors_static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make parameters for the static model visitors (no visitors) — setup_visitors_static","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_weather_forced.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the forced model for weather — setup_weather_forced","title":"Set up the forced model for weather — setup_weather_forced","text":"Set forced model weather","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_weather_forced.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the forced model for weather — setup_weather_forced","text":"","code":"setup_weather_forced(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_weather_forced.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the forced model for weather — setup_weather_forced","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_weather_forced.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the forced model for weather — setup_weather_forced","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_weather_null.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up the null model for weather — setup_weather_null","title":"Set up the null model for weather — setup_weather_null","text":"Set null model weather","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_weather_null.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up the null model for weather — setup_weather_null","text":"","code":"setup_weather_null(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/setup_weather_null.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up the null model for weather — setup_weather_null","text":"pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/setup_weather_null.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up the null model for weather — setup_weather_null","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/shapeIt.html","id":null,"dir":"Reference","previous_headings":"","what":"Check the shape and dimensions of an object — shapeIt","title":"Check the shape and dimensions of an object — shapeIt","text":"Check shape dimensions object","code":""},{"path":"https://dd-harp.github.io/exDE/reference/shapeIt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check the shape and dimensions of an object — shapeIt","text":"","code":"shapeIt(obj, d1, d2)"},{"path":"https://dd-harp.github.io/exDE/reference/shapeIt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check the shape and dimensions of an object — shapeIt","text":"obj numeric object d1 integer d2 integer","code":""},{"path":"https://dd-harp.github.io/exDE/reference/shapeIt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check the shape and dimensions of an object — shapeIt","text":"matrix","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.eir.html","id":null,"dir":"Reference","previous_headings":"","what":"A model for travel malaria based on the eir in destinations — travel_malaria.eir","title":"A model for travel malaria based on the eir in destinations — travel_malaria.eir","text":"Implements travel_malaria model eir-based model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.eir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A model for travel malaria based on the eir in destinations — travel_malaria.eir","text":"","code":"# S3 method for eir travel_malaria(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.eir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A model for travel malaria based on the eir in destinations — travel_malaria.eir","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.eir.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A model for travel malaria based on the eir in destinations — travel_malaria.eir","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.foi.html","id":null,"dir":"Reference","previous_headings":"","what":"A model for the travel FoI — travel_malaria.foi","title":"A model for the travel FoI — travel_malaria.foi","text":"Implements travel_malaria model travel FoI","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.foi.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A model for the travel FoI — travel_malaria.foi","text":"","code":"# S3 method for foi travel_malaria(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.foi.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A model for the travel FoI — travel_malaria.foi","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.foi.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"A model for the travel FoI — travel_malaria.foi","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulate travel malaria — travel_malaria","title":"Simulate travel malaria — travel_malaria","text":"method dispatches type pars$TRAVEL.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulate travel malaria — travel_malaria","text":"","code":"travel_malaria(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simulate travel malaria — travel_malaria","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simulate travel malaria — travel_malaria","text":"travel FoI, numeric value","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.static.html","id":null,"dir":"Reference","previous_headings":"","what":"travel, a static model — travel_malaria.static","title":"travel, a static model — travel_malaria.static","text":"Implements travel_malaria static model (nothing)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.static.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"travel, a static model — travel_malaria.static","text":"","code":"# S3 method for static travel_malaria(t, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.static.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"travel, a static model — travel_malaria.static","text":"t current simulation time pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/travel_malaria.static.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"travel, a static model — travel_malaria.static","text":"numeric","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the initial values to the last values of the last simulation — update_inits","title":"Set the initial values to the last values of the last simulation — update_inits","text":"Set initial values last values last simulation","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the initial values to the last values of the last simulation — update_inits","text":"","code":"update_inits(y0, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the initial values to the last values of the last simulation — update_inits","text":"y0 vector initial values pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the initial values to the last values of the last simulation — update_inits","text":"y numeric vector","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.basic.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for the basic aquatic mosquito competition model — update_inits_L.basic","title":"Update inits for the basic aquatic mosquito competition model — update_inits_L.basic","text":"Update inits basic aquatic mosquito competition model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.basic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for the basic aquatic mosquito competition model — update_inits_L.basic","text":"","code":"# S3 method for basic update_inits_L(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.basic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for the basic aquatic mosquito competition model — update_inits_L.basic","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.basic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for the basic aquatic mosquito competition model — update_inits_L.basic","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the initial values from a vector of model states — update_inits_L","title":"Set the initial values from a vector of model states — update_inits_L","text":"method dispatches type pars$Lpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the initial values from a vector of model states — update_inits_L","text":"","code":"update_inits_L(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the initial values from a vector of model states — update_inits_L","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the initial values from a vector of model states — update_inits_L","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for the basic aquatic mosquito competition model — update_inits_L.trace","title":"Update inits for the basic aquatic mosquito competition model — update_inits_L.trace","text":"Update inits basic aquatic mosquito competition model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for the basic aquatic mosquito competition model — update_inits_L.trace","text":"","code":"# S3 method for trace update_inits_L(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for the basic aquatic mosquito competition model — update_inits_L.trace","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_L.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for the basic aquatic mosquito competition model — update_inits_L.trace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.GeRM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Update the initial values for GeRM adult mosquito model — update_inits_MYZ.GeRM_dde","title":"Update the initial values for GeRM adult mosquito model — update_inits_MYZ.GeRM_dde","text":"Update initial values GeRM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.GeRM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update the initial values for GeRM adult mosquito model — update_inits_MYZ.GeRM_dde","text":"","code":"# S3 method for GeRM_dde update_inits_MYZ(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.GeRM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update the initial values for GeRM adult mosquito model — update_inits_MYZ.GeRM_dde","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.GeRM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update the initial values for GeRM adult mosquito model — update_inits_MYZ.GeRM_dde","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.GeRM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for GeRM adult mosquito model — update_inits_MYZ.GeRM_ode","title":"Make inits for GeRM adult mosquito model — update_inits_MYZ.GeRM_ode","text":"Make inits GeRM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.GeRM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for GeRM adult mosquito model — update_inits_MYZ.GeRM_ode","text":"","code":"# S3 method for GeRM_ode update_inits_MYZ(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.GeRM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for GeRM adult mosquito model — update_inits_MYZ.GeRM_ode","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.GeRM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for GeRM adult mosquito model — update_inits_MYZ.GeRM_ode","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.Gtrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for Gtrace — update_inits_MYZ.Gtrace","title":"Update inits for Gtrace — update_inits_MYZ.Gtrace","text":"Update inits Gtrace","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.Gtrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for Gtrace — update_inits_MYZ.Gtrace","text":"","code":"# S3 method for Gtrace update_inits_MYZ(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.Gtrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for Gtrace — update_inits_MYZ.Gtrace","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.Gtrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for Gtrace — update_inits_MYZ.Gtrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.RM_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for RM adult mosquito model — update_inits_MYZ.RM_dde","title":"Update inits for RM adult mosquito model — update_inits_MYZ.RM_dde","text":"Update inits RM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.RM_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for RM adult mosquito model — update_inits_MYZ.RM_dde","text":"","code":"# S3 method for RM_dde update_inits_MYZ(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.RM_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for RM adult mosquito model — update_inits_MYZ.RM_dde","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.RM_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for RM adult mosquito model — update_inits_MYZ.RM_dde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.RM_ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for RM adult mosquito model — update_inits_MYZ.RM_ode","title":"Make inits for RM adult mosquito model — update_inits_MYZ.RM_ode","text":"Make inits RM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.RM_ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for RM adult mosquito model — update_inits_MYZ.RM_ode","text":"","code":"# S3 method for RM_ode update_inits_MYZ(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.RM_ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for RM adult mosquito model — update_inits_MYZ.RM_ode","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.RM_ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for RM adult mosquito model — update_inits_MYZ.RM_ode","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.Ztrace.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for Ztrace — update_inits_MYZ.Ztrace","title":"Update inits for Ztrace — update_inits_MYZ.Ztrace","text":"Update inits Ztrace","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.Ztrace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for Ztrace — update_inits_MYZ.Ztrace","text":"","code":"# S3 method for Ztrace update_inits_MYZ(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.Ztrace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for Ztrace — update_inits_MYZ.Ztrace","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.Ztrace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for Ztrace — update_inits_MYZ.Ztrace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.basicM.html","id":null,"dir":"Reference","previous_headings":"","what":"Make inits for RM adult mosquito model — update_inits_MYZ.basicM","title":"Make inits for RM adult mosquito model — update_inits_MYZ.basicM","text":"Make inits RM adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.basicM.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make inits for RM adult mosquito model — update_inits_MYZ.basicM","text":"","code":"# S3 method for basicM update_inits_MYZ(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.basicM.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make inits for RM adult mosquito model — update_inits_MYZ.basicM","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.basicM.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make inits for RM adult mosquito model — update_inits_MYZ.basicM","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the initial values as a vector — update_inits_MYZ","title":"Set the initial values as a vector — update_inits_MYZ","text":"method dispatches type pars$MYZpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the initial values as a vector — update_inits_MYZ","text":"","code":"update_inits_MYZ(pars, y0, s)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the initial values as a vector — update_inits_MYZ","text":"pars list y0 vector variable values simulation s species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_MYZ.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the initial values as a vector — update_inits_MYZ","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for the SIP human model from a vector of states — update_inits_X.SIP","title":"Update inits for the SIP human model from a vector of states — update_inits_X.SIP","text":"Update inits SIP human model vector states","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for the SIP human model from a vector of states — update_inits_X.SIP","text":"","code":"# S3 method for SIP update_inits_X(pars, y0, i)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for the SIP human model from a vector of states — update_inits_X.SIP","text":"pars list y0 vector initial values host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.SIP.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for the SIP human model from a vector of states — update_inits_X.SIP","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for the SIS human model from a vector of states — update_inits_X.SIS","title":"Update inits for the SIS human model from a vector of states — update_inits_X.SIS","text":"Update inits SIS human model vector states","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for the SIS human model from a vector of states — update_inits_X.SIS","text":"","code":"# S3 method for SIS update_inits_X(pars, y0, i)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for the SIS human model from a vector of states — update_inits_X.SIS","text":"pars list y0 vector initial values host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.SIS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for the SIS human model from a vector of states — update_inits_X.SIS","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.hMoI.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for hybrid MoI human model from a vector of states — update_inits_X.hMoI","title":"Update inits for hybrid MoI human model from a vector of states — update_inits_X.hMoI","text":"Update inits hybrid MoI human model vector states","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.hMoI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for hybrid MoI human model from a vector of states — update_inits_X.hMoI","text":"","code":"# S3 method for hMoI update_inits_X(pars, y0, i)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.hMoI.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for hybrid MoI human model from a vector of states — update_inits_X.hMoI","text":"pars list y0 vector initial values host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.hMoI.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for hybrid MoI human model from a vector of states — update_inits_X.hMoI","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.html","id":null,"dir":"Reference","previous_headings":"","what":"Set the initial values from a vector of states — update_inits_X","title":"Set the initial values from a vector of states — update_inits_X","text":"method dispatches type pars$Xpar.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set the initial values from a vector of states — update_inits_X","text":"","code":"update_inits_X(pars, y0, i)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set the initial values from a vector of states — update_inits_X","text":"pars list y0 vector initial values host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set the initial values from a vector of states — update_inits_X","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.trace.html","id":null,"dir":"Reference","previous_headings":"","what":"Update inits for the trace human model from a vector of states — update_inits_X.trace","title":"Update inits for the trace human model from a vector of states — update_inits_X.trace","text":"Update inits trace human model vector states","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.trace.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update inits for the trace human model from a vector of states — update_inits_X.trace","text":"","code":"# S3 method for trace update_inits_X(pars, y0, i)"},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.trace.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update inits for the trace human model from a vector of states — update_inits_X.trace","text":"pars list y0 vector initial values host species index","code":""},{"path":"https://dd-harp.github.io/exDE/reference/update_inits_X.trace.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update inits for the trace human model from a vector of states — update_inits_X.trace","text":"none","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn.html","id":null,"dir":"Reference","previous_headings":"","what":"Generalized spatial differential equation model — xDE_diffeqn","title":"Generalized spatial differential equation model — xDE_diffeqn","text":"Compute derivatives deSolve::ode deSolve::dede using generic methods model component.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generalized spatial differential equation model — xDE_diffeqn","text":"","code":"xDE_diffeqn(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generalized spatial differential equation model — xDE_diffeqn","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generalized spatial differential equation model — xDE_diffeqn","text":"list containing vector state derivatives","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_aquatic.html","id":null,"dir":"Reference","previous_headings":"","what":"Differential equation models for aquatic mosquito populations — xDE_diffeqn_aquatic","title":"Differential equation models for aquatic mosquito populations — xDE_diffeqn_aquatic","text":"Compute derivatives deSolve::ode deSolve::dede using generic methods model component.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_aquatic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Differential equation models for aquatic mosquito populations — xDE_diffeqn_aquatic","text":"","code":"xDE_diffeqn_aquatic(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_aquatic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Differential equation models for aquatic mosquito populations — xDE_diffeqn_aquatic","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_aquatic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Differential equation models for aquatic mosquito populations — xDE_diffeqn_aquatic","text":"list containing vector state derivatives","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_cohort.html","id":null,"dir":"Reference","previous_headings":"","what":"Differential equation models for human cohorts — xDE_diffeqn_cohort","title":"Differential equation models for human cohorts — xDE_diffeqn_cohort","text":"Compute derivatives deSolve::ode deSolve::dede using generic methods model component.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_cohort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Differential equation models for human cohorts — xDE_diffeqn_cohort","text":"","code":"xDE_diffeqn_cohort(a, y, pars, F_eir)"},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_cohort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Differential equation models for human cohorts — xDE_diffeqn_cohort","text":"age cohort y state vector pars list F_eir trace function returns eir","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_cohort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Differential equation models for human cohorts — xDE_diffeqn_cohort","text":"list containing vector state derivatives","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_human.html","id":null,"dir":"Reference","previous_headings":"","what":"Differential equations isolating the humans, forced with Ztrace — xDE_diffeqn_human","title":"Differential equations isolating the humans, forced with Ztrace — xDE_diffeqn_human","text":"Compute derivatives deSolve::ode deSolve::dede using generic methods model component.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_human.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Differential equations isolating the humans, forced with Ztrace — xDE_diffeqn_human","text":"","code":"xDE_diffeqn_human(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_human.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Differential equations isolating the humans, forced with Ztrace — xDE_diffeqn_human","text":"t current simulation time y state vector pars list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_human.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Differential equations isolating the humans, forced with Ztrace — xDE_diffeqn_human","text":"list containing vector state derivatives","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_mosy.html","id":null,"dir":"Reference","previous_headings":"","what":"Generalized spatial differential equation model (mosquito only) — xDE_diffeqn_mosy","title":"Generalized spatial differential equation model (mosquito only) — xDE_diffeqn_mosy","text":"Mirrors xDE_diffeqn includes adult aquatic mosquito components.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_mosy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generalized spatial differential equation model (mosquito only) — xDE_diffeqn_mosy","text":"","code":"xDE_diffeqn_mosy(t, y, pars)"},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_mosy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generalized spatial differential equation model (mosquito only) — xDE_diffeqn_mosy","text":"t current simulation time y state vector pars list appropriate adult mosquito model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xDE_diffeqn_mosy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generalized spatial differential equation model (mosquito only) — xDE_diffeqn_mosy","text":"list containing vector state derivatives","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_EIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the EIR vs. time — xde_lines_EIR","title":"Add lines for the EIR vs. time — xde_lines_EIR","text":"Add lines EIR vs. time","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_EIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the EIR vs. time — xde_lines_EIR","text":"","code":"xde_lines_EIR(tm, EIR, nStrata, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_EIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the EIR vs. time — xde_lines_EIR","text":"tm time EIR entomological inoculation rate nStrata number human / host population strata clrs vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_M.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for adult mosquito population density — xde_lines_M","title":"Add lines for adult mosquito population density — xde_lines_M","text":"Add lines adult mosquito population density","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_M.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for adult mosquito population density — xde_lines_M","text":"","code":"xde_lines_M(MYZ, pars, clrs = \"darkblue\", llty = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_M.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for adult mosquito population density — xde_lines_M","text":"MYZ list output exDE::parse_deout() pars list defines exDE model (e.g.,  generated xde_setup()) clrs vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_PR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the prevalence / parasite rate (PR) from a model of human infection and immunity — xde_lines_PR","title":"Add lines for the prevalence / parasite rate (PR) from a model of human infection and immunity — xde_lines_PR","text":"Add lines prevalence / parasite rate (PR) model human infection immunity","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_PR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the prevalence / parasite rate (PR) from a model of human infection and immunity — xde_lines_PR","text":"","code":"xde_lines_PR(tm, PR, nStrata, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_PR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the prevalence / parasite rate (PR) from a model of human infection and immunity — xde_lines_PR","text":"tm time PR computed parasite rate nStrata number human / host population strata clrs vector colors llty integer (integers) specifies lty plotting","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_X_SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the density of infected individuals for the SIP model — xde_lines_X_SIP","title":"Add lines for the density of infected individuals for the SIP model — xde_lines_X_SIP","text":"Add lines density infected individuals SIP model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_X_SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the density of infected individuals for the SIP model — xde_lines_X_SIP","text":"","code":"xde_lines_X_SIP(   XH,   pars,   clrs = c(\"darkblue\", \"darkred\", \"darkgreen\"),   llty = 1 )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_X_SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the density of infected individuals for the SIP model — xde_lines_X_SIP","text":"XH list outputs parse_deout_X_SIS pars list defines exDE model (e.g.,  generated xde_setup()) clrs vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_X_SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the density of infected individuals for the SIS model — xde_lines_X_SIS","title":"Add lines for the density of infected individuals for the SIS model — xde_lines_X_SIS","text":"Add lines density infected individuals SIS model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_X_SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the density of infected individuals for the SIS model — xde_lines_X_SIS","text":"","code":"xde_lines_X_SIS(XH, nStrata, clrs = c(\"darkblue\", \"darkred\"), llty = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_X_SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the density of infected individuals for the SIS model — xde_lines_X_SIS","text":"XH list outputs parse_deout_X_SIS nStrata number population strata clrs vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_YZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the density of infected and infective mosquitoes — xde_lines_YZ","title":"Add lines for the density of infected and infective mosquitoes — xde_lines_YZ","text":"Add lines density infected infective mosquitoes","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_YZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the density of infected and infective mosquitoes — xde_lines_YZ","text":"","code":"xde_lines_YZ(MYZ, pars, Yclrs = \"purple\", Zclrs = \"darkred\", llty = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_YZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the density of infected and infective mosquitoes — xde_lines_YZ","text":"MYZ list output exDE::parse_deout() pars list defines exDE model (e.g.,  generated xde_setup()) Yclrs vector colors Zclrs vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_YZ_fracs.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the fraction of infected and infective mosquitoes — xde_lines_YZ_fracs","title":"Add lines for the fraction of infected and infective mosquitoes — xde_lines_YZ_fracs","text":"Add lines fraction infected infective mosquitoes","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_YZ_fracs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the fraction of infected and infective mosquitoes — xde_lines_YZ_fracs","text":"","code":"xde_lines_YZ_fracs(MYZ, pars, Yclrs = \"purple\", Zclrs = \"darkred\", llty = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_YZ_fracs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the fraction of infected and infective mosquitoes — xde_lines_YZ_fracs","text":"MYZ list output exDE::parse_deout() pars list defines exDE model (e.g.,  generated xde_setup()) Yclrs vector colors infected mosquitoes Zclrs vector colors infective mosquitoes llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_aEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Add lines for the annualized EIR vs. t — xde_lines_aEIR","title":"Add lines for the annualized EIR vs. t — xde_lines_aEIR","text":"Add lines annualized EIR vs. t","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_aEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add lines for the annualized EIR vs. t — xde_lines_aEIR","text":"","code":"xde_lines_aEIR(tm, EIR, nStrata, clrs = \"black\", llty = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_lines_aEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add lines for the annualized EIR vs. t — xde_lines_aEIR","text":"tm time EIR entomological inoculation rate nStrata number human / host population strata clrs vector colors llty integer (integers) set lty plotting","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_EIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the EIR vs. time — xde_plot_EIR","title":"Plot the EIR vs. time — xde_plot_EIR","text":"Plot EIR vs. time","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_EIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the EIR vs. time — xde_plot_EIR","text":"","code":"xde_plot_EIR(   pars,   i = 1,   clrs = \"black\",   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_EIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the EIR vs. time — xde_plot_EIR","text":"pars list defines exDE model (e.g.,  generated exDE::xde_setup()) host species index clrs vector colors llty integer (integers) set lty plotting stable logical: set FALSE orbits TRUE stable_orbits add_axes logical: plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_M.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot adult mosquito population density — xde_plot_M","title":"Plot adult mosquito population density — xde_plot_M","text":"Plot adult mosquito population density","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_M.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot adult mosquito population density — xde_plot_M","text":"","code":"xde_plot_M(   pars,   s = 1,   clrs = \"darkblue\",   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_M.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot adult mosquito population density — xde_plot_M","text":"pars list defines exDE model (e.g.,  generated xde_setup()) s vector species index clrs vector colors llty integer (integers) set lty plotting stable logical: set FALSE orbits TRUE stable_orbits add_axes logical: plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_PR.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the prevalence / parasite rate (PR) from a model of human infection and immunity — xde_plot_PR","title":"Plot the prevalence / parasite rate (PR) from a model of human infection and immunity — xde_plot_PR","text":"Plot prevalence / parasite rate (PR) model human infection immunity","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_PR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the prevalence / parasite rate (PR) from a model of human infection and immunity — xde_plot_PR","text":"","code":"xde_plot_PR(   pars,   i = 1,   clrs = \"black\",   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_PR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the prevalence / parasite rate (PR) from a model of human infection and immunity — xde_plot_PR","text":"pars list defines exDE model (e.g.,  generated xde_setup()) host species index clrs vector colors llty integer (integers) specifies lty plotting stable logical: set FALSE orbits TRUE stable_orbits add_axes logical: plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.SIP.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the density of infected individuals for the SIP model — xde_plot_X.SIP","title":"Plot the density of infected individuals for the SIP model — xde_plot_X.SIP","text":"Plot density infected individuals SIP model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.SIP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the density of infected individuals for the SIP model — xde_plot_X.SIP","text":"","code":"# S3 method for SIP xde_plot_X(   pars,   i = 1,   clrs = c(\"darkblue\", \"darkred\", \"darkgreen\"),   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.SIP.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the density of infected individuals for the SIP model — xde_plot_X.SIP","text":"pars list defines exDE model (e.g.,  generated xde_setup()) host species index clrs vector colors llty integer (integers) set lty plotting stable logical: set FALSE orbits TRUE stable_orbits add_axes logical: plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.SIS.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the density of infected individuals for the SIS model — xde_plot_X.SIS","title":"Plot the density of infected individuals for the SIS model — xde_plot_X.SIS","text":"Plot density infected individuals SIS model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.SIS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the density of infected individuals for the SIS model — xde_plot_X.SIS","text":"","code":"# S3 method for SIS xde_plot_X(   pars,   i = 1,   clrs = c(\"darkblue\", \"darkred\"),   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.SIS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the density of infected individuals for the SIS model — xde_plot_X.SIS","text":"pars list defines exDE model (e.g.,  generated xde_setup()) host species index clrs vector colors llty integer (integers) set lty plotting stable logical: set FALSE orbits TRUE stable_orbits add_axes logical: plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic plotting for epidemiological models — xde_plot_X","title":"Basic plotting for epidemiological models — xde_plot_X","text":"Basic plotting epidemiological models","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Basic plotting for epidemiological models — xde_plot_X","text":"","code":"xde_plot_X(   pars,   i = 1,   clrs = \"black\",   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_X.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Basic plotting for epidemiological models — xde_plot_X","text":"pars list defines exDE model (e.g.,  generated xde_setup()) host species index clrs vector colors llty integer (integers) set lty plotting stable logical: set FALSE orbits TRUE stable_orbits add_axes logical: plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_YZ.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the density of infected and infective mosquitoes — xde_plot_YZ","title":"Plot the density of infected and infective mosquitoes — xde_plot_YZ","text":"Plot density infected infective mosquitoes","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_YZ.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the density of infected and infective mosquitoes — xde_plot_YZ","text":"","code":"xde_plot_YZ(   pars,   s = 1,   Yclrs = \"purple\",   Zclrs = \"darkred\",   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_YZ.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the density of infected and infective mosquitoes — xde_plot_YZ","text":"pars list defines exDE model (e.g.,  generated xde_setup()) s vector species index Yclrs vector colors infected mosquitoes Zclrs vector colors infective mosquitoes llty integer (integers) set lty plotting stable set FALSE orbits TRUE stable_orbits add_axes plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_YZ_fracs.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the fraction of infected and infective mosquitoes — xde_plot_YZ_fracs","title":"Plot the fraction of infected and infective mosquitoes — xde_plot_YZ_fracs","text":"Plot fraction infected infective mosquitoes","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_YZ_fracs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the fraction of infected and infective mosquitoes — xde_plot_YZ_fracs","text":"","code":"xde_plot_YZ_fracs(   pars,   s = 1,   Yclrs = \"purple\",   Zclrs = \"darkred\",   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_YZ_fracs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the fraction of infected and infective mosquitoes — xde_plot_YZ_fracs","text":"pars list defines exDE model (e.g.,  generated xde_setup()) s vector species index Yclrs vector colors infected mosquitoes Zclrs vector colors infective mosquitoes llty integer (integers) set lty plotting stable logical, set FALSE orbits TRUE stable_orbits add_axes logical plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_aEIR.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the annualized EIR vs. time — xde_plot_aEIR","title":"Plot the annualized EIR vs. time — xde_plot_aEIR","text":"Plot annualized EIR vs. time","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_aEIR.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the annualized EIR vs. time — xde_plot_aEIR","text":"","code":"xde_plot_aEIR(   pars,   i = 1,   clrs = \"black\",   llty = 1,   stable = FALSE,   add_axes = TRUE )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_plot_aEIR.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the annualized EIR vs. time — xde_plot_aEIR","text":"pars list defines exDE model (e.g.,  generated exDE::xde_setup()) host species index clrs vector colors llty integer (integers) set lty plotting stable logical: set FALSE orbits TRUE stable_orbits add_axes logical: plot axes TRUE","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up a model for xde_diffeqn — xde_setup","title":"Set up a model for xde_diffeqn — xde_setup","text":"Set model xde_diffeqn","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up a model for xde_diffeqn — xde_setup","text":"","code":"xde_setup(   modelName = \"unnamed\",   MYZname = \"RM\",   Xname = \"SIS\",   Lname = \"trace\",   nPatches = 1,   nVectors = 1,   nHosts = 1,   HPop = 1000,   membership = 1,   MYZopts = list(),   calK = \"herethere\",   calKopts = list(),   EIPname = \"static\",   EIPopts = list(),   Xopts = list(),   BFopts = list(),   residence = 1,   searchB = 1,   F_circadian = NULL,   TimeSpent = \"athome\",   TimeSpentOpts = list(),   searchQ = 1,   Lopts = list() )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up a model for xde_diffeqn — xde_setup","text":"modelName name model (arbitrary) MYZname character string defining MYZ model Xname character string defining X model Lname character string defining L model nPatches number patches nVectors number vector species nHosts number vertebrate host species HPop number humans patch membership vector describes patch aquatic habitat found MYZopts list configure MYZ model calK either calK matrix string defines set calKopts options setup calK EIPname options setup EIPmod EIPopts options setup EIPmod Xopts list configure X model BFopts list configure blood feeding model residence vector describes patch human stratum lives searchB vector search weights blood feeding F_circadian function describing mosquito daily activity TimeSpent either TimeSpent matrix string call function sets TimeSpentOpts options setup TimeSpent searchQ vector search weights egg laying Lopts list configure L model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up a model for xde_diffeqn — xde_setup","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_aquatic.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up a model for xde_diffeqn_aqua — xde_setup_aquatic","title":"Set up a model for xde_diffeqn_aqua — xde_setup_aquatic","text":"Set model xde_diffeqn_aqua","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_aquatic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up a model for xde_diffeqn_aqua — xde_setup_aquatic","text":"","code":"xde_setup_aquatic(   modelName = \"unnamed\",   nHabitats = 1,   nVectors = 1,   Lname = \"basic\",   Lopts = list(),   MYZopts = list(),   LSMname = \"null\" )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_aquatic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up a model for xde_diffeqn_aqua — xde_setup_aquatic","text":"modelName name model (arbitrary) nHabitats number habitats nVectors number vector species Lname character string defining L model Lopts list configure L model MYZopts list configure F_eggs Gtrace model LSMname character string defining LSM model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_aquatic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up a model for xde_diffeqn_aqua — xde_setup_aquatic","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_cohort.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up a model for xde_diffeqn_cohort — xde_setup_cohort","title":"Set up a model for xde_diffeqn_cohort — xde_setup_cohort","text":"Set model xde_diffeqn_cohort","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_cohort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up a model for xde_diffeqn_cohort — xde_setup_cohort","text":"","code":"xde_setup_cohort(   F_eir,   modelName = \"unnamed\",   Xname = \"SIS\",   HPop = 1000,   searchB = 1,   residence = 1,   Xopts = list() )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_cohort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up a model for xde_diffeqn_cohort — xde_setup_cohort","text":"F_eir function F_eir(t, pars) returns daily FoI modelName name model (arbitrary) Xname character string defining X model HPop number humans patch searchB vector search weights blood feeding residence vector describes patch human stratum lives Xopts list configure X model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_cohort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up a model for xde_diffeqn_cohort — xde_setup_cohort","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_human.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up a model for xde_diffeqn_human — xde_setup_human","title":"Set up a model for xde_diffeqn_human — xde_setup_human","text":"Set model xde_diffeqn_human","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_human.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up a model for xde_diffeqn_human — xde_setup_human","text":"","code":"xde_setup_human(   modelName = \"unnamed\",   Xname = \"SIS\",   HPop = 1000,   MYZopts = list(),   Xopts = list(),   BFopts = list(),   residence = 1,   searchB = 1,   F_circadian = NULL,   TimeSpent = \"athome\",   TimeSpentOpts = list() )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_human.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up a model for xde_diffeqn_human — xde_setup_human","text":"modelName name model (arbitrary) Xname character string defining X model HPop number humans patch MYZopts list configure MYZ model Xopts list configure X model BFopts list configure blood feeding model residence vector describes patch human stratum lives searchB vector search weights blood feeding F_circadian function describing mosquito daily activity TimeSpent either TimeSpent matrix string call function sets TimeSpentOpts options setup TimeSpent","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_human.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up a model for xde_diffeqn_human — xde_setup_human","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_mosy.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up a model for xde_diffeqn_mosy — xde_setup_mosy","title":"Set up a model for xde_diffeqn_mosy — xde_setup_mosy","text":"Set model xde_diffeqn_mosy","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_mosy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up a model for xde_diffeqn_mosy — xde_setup_mosy","text":"","code":"xde_setup_mosy(   modelName = \"unnamed\",   MYZname = \"basicM\",   Lname = \"basic\",   nPatches = 1,   nVectors = 1,   membership = 1,   MYZopts = list(),   calK = \"herethere\",   calKopts = list(),   searchQ = 1,   Lopts = list(),   kappa = NULL )"},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_mosy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up a model for xde_diffeqn_mosy — xde_setup_mosy","text":"modelName name model (arbitrary) MYZname character string defining MYZ model Lname character string defining L model nPatches number patches nVectors number vector species membership vector describes patch aquatic habitat found MYZopts list configure MYZ model calK either calK matrix string defines set calKopts options setup calK searchQ vector search weights egg laying Lopts list configure L model kappa values -- net infectivity force adult infection dynamics","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_setup_mosy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set up a model for xde_diffeqn_mosy — xde_setup_mosy","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.aqua.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua","title":"Solve a system of equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua","text":"Implements xde_solve aquatic dynaamic","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.aqua.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua","text":"","code":"# S3 method for aqua xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.aqua.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.aqua.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.aqua_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of delay equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua_dde","title":"Solve a system of delay equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua_dde","text":"Implements xde_solve aquatic dynaamic","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.aqua_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of delay equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua_dde","text":"","code":"# S3 method for aqua_dde xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.aqua_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of delay equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua_dde","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.aqua_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of delay equations for aquatic dynamics, forced by egg deposition, using xDE_diffeqn_aquatic — xde_solve.aqua_dde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.cohort.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of equations with xDE_diffeqn_cohort — xde_solve.cohort","title":"Solve a system of equations with xDE_diffeqn_cohort — xde_solve.cohort","text":"Implements xde_solve mosquito dynamics (transmission)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.cohort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of equations with xDE_diffeqn_cohort — xde_solve.cohort","text":"","code":"# S3 method for cohort xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.cohort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of equations with xDE_diffeqn_cohort — xde_solve.cohort","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.cohort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of equations with xDE_diffeqn_cohort — xde_solve.cohort","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of equations as a dde — xde_solve.dde","title":"Solve a system of equations as a dde — xde_solve.dde","text":"Implements xde_solve delay differential equations","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of equations as a dde — xde_solve.dde","text":"","code":"# S3 method for dde xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of equations as a dde — xde_solve.dde","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of equations as a dde — xde_solve.dde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of equations — xde_solve","title":"Solve a system of equations — xde_solve","text":"method dispatches type pars$xde.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of equations — xde_solve","text":"","code":"xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of equations — xde_solve","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of equations — xde_solve","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.human.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of equations with xDE_diffeqn_human — xde_solve.human","title":"Solve a system of equations with xDE_diffeqn_human — xde_solve.human","text":"Implements xde_solve mosquito dynamics (transmission)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.human.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of equations with xDE_diffeqn_human — xde_solve.human","text":"","code":"# S3 method for human xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.human.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of equations with xDE_diffeqn_human — xde_solve.human","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.human.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of equations with xDE_diffeqn_human — xde_solve.human","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.mosy.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy","title":"Solve a system of equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy","text":"Implements xde_solve mosquito dynamics (transmission)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.mosy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy","text":"","code":"# S3 method for mosy xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.mosy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.mosy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.mosy_dde.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of delay differential equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy_dde","title":"Solve a system of delay differential equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy_dde","text":"Implements xde_solve mosquito dynamics (transmission)","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.mosy_dde.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of delay differential equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy_dde","text":"","code":"# S3 method for mosy_dde xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.mosy_dde.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of delay differential equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy_dde","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.mosy_dde.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of delay differential equations for mosquito ecology using xDE_diffeqn_mosy — xde_solve.mosy_dde","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.ode.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve a system of equations as an ode — xde_solve.ode","title":"Solve a system of equations as an ode — xde_solve.ode","text":"Implements xde_solve ordinary differential equations","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.ode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve a system of equations as an ode — xde_solve.ode","text":"","code":"# S3 method for ode xde_solve(pars, Tmax = 365, dt = 1)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.ode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve a system of equations as an ode — xde_solve.ode","text":"pars list defines model Tmax last time point, run 0...Tmax dt time interval outputs","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_solve.ode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve a system of equations as an ode — xde_solve.ode","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_stable_orbit.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve for the steady state or stable orbit of a system of equations — xde_stable_orbit","title":"Solve for the steady state or stable orbit of a system of equations — xde_stable_orbit","text":"method dispatches type pars$xde.","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_stable_orbit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve for the steady state or stable orbit of a system of equations — xde_stable_orbit","text":"","code":"xde_stable_orbit(pars, Ymax = 10)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_stable_orbit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve for the steady state or stable orbit of a system of equations — xde_stable_orbit","text":"pars list defines model Ymax number years burn-","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_stable_orbit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve for the steady state or stable orbit of a system of equations — xde_stable_orbit","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_steady.html","id":null,"dir":"Reference","previous_headings":"","what":"Solve for the steady state of a system of equations using rootSolve::steady — xde_steady","title":"Solve for the steady state of a system of equations using rootSolve::steady — xde_steady","text":"method dispatches type pars$xde","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_steady.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Solve for the steady state of a system of equations using rootSolve::steady — xde_steady","text":"","code":"xde_steady(pars)"},{"path":"https://dd-harp.github.io/exDE/reference/xde_steady.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Solve for the steady state of a system of equations using rootSolve::steady — xde_steady","text":"pars list defines model","code":""},{"path":"https://dd-harp.github.io/exDE/reference/xde_steady.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Solve for the steady state of a system of equations using rootSolve::steady — xde_steady","text":"list","code":""},{"path":"https://dd-harp.github.io/exDE/news/index.html","id":"exde-100","dir":"Changelog","previous_headings":"","what":"exDE 1.0.0","title":"exDE 1.0.0","text":"CRAN release: 2022-11-18 Extensive update include exogenous forcing weather, climate, etc. well vector control, including ITN-based model vector control Extended documentation Extended testing Include CITATION file pre-print Re-submit CRAN","code":""},{"path":"https://dd-harp.github.io/exDE/news/index.html","id":"exde-010","dir":"Changelog","previous_headings":"","what":"exDE 0.1.0","title":"exDE 0.1.0","text":"Initial release exDE CRAN.","code":""}]
diff --git a/sitemap.xml b/sitemap.xml
index daa6fd64..0731eff9 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -759,6 +759,21 @@
   <url>
     <loc>https://dd-harp.github.io/exDE/reference/compute_terms_steady.html</loc>
   </url>
+  <url>
+    <loc>https://dd-harp.github.io/exDE/reference/compute_vars_aqua.html</loc>
+  </url>
+  <url>
+    <loc>https://dd-harp.github.io/exDE/reference/compute_vars_cohort.html</loc>
+  </url>
+  <url>
+    <loc>https://dd-harp.github.io/exDE/reference/compute_vars_full.html</loc>
+  </url>
+  <url>
+    <loc>https://dd-harp.github.io/exDE/reference/compute_vars_human.html</loc>
+  </url>
+  <url>
+    <loc>https://dd-harp.github.io/exDE/reference/compute_vars_mosy.html</loc>
+  </url>
   <url>
     <loc>https://dd-harp.github.io/exDE/reference/dEIPdt.html</loc>
   </url>