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 @@

The long wayexDE::make_indices.

 params$max_ix = 0 
-params = make_indices(params)
+params = make_indices(params) +params$nHosts = 0

Then we can set up the initial conditions vector and use deSolve::ode to solve the model. Normally these values would be computed within exDE::xDE_diffeqn. 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 index c8e89d25..6b9cab77 100644 Binary files a/articles/vc_lemenach_files/figure-html/unnamed-chunk-14-1.png and b/articles/vc_lemenach_files/figure-html/unnamed-chunk-14-1.png differ 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 @@ -A model for exposure. The function F_b must be define — Exposure • exDEExposure and Infection — Exposure • exDE @@ -70,13 +80,18 @@

-

A model for exposure. The function F_b must be define

+

Exposure and Infection

Source: R/exposure.R
Exposure.Rd
-

A model for exposure. The function F_b must be define

+

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.

@@ -91,18 +106,18 @@

Argumentslist

+

the model object as a list

Value

-

list

+

the function modifies pars and returns it: the computed FoI are stored as pars$FoI

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 @@ -A model for exposure — F_foi • exDEA model for daily FoI as a function of the daily EIR. — F_foi • exDE @@ -70,13 +82,19 @@
-

A model for exposure

+

A model for daily FoI as a function of the daily EIR.

Source: R/exposure.R
F_foi.Rd
-

This method dispatches on the type of pars$FOIpar.

+

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.

@@ -87,7 +105,7 @@

Usage

Arguments

eir
-

the daily eir

+

the daily eir for each stratum

b
@@ -95,14 +113,14 @@

Argumentslist

+

the model object as a list

Value

-

see help pages for specific methods

+

the daily, local force of infection as a numeric vector