Initial Commit

R Package Structure
Add calc_birdflow_mc()

.Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$

.gitattributes

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+# Basic .gitattributes for a R repo.
+# From: https://github.com/alexkaratarakis/gitattributes/blob/master/R.gitattributes
+# Modified slightly
+
+# Source files
+# ============
+*.Rdata binary
+*.RData binary
+*.rda   binary
+*.rdb   binary
+*.rds   binary
+*.Rd    text
+*.Rdx   binary
+*.Rmd	  text
+*.md    text
+*.R  	  text
+*.Rproj text

.gitignore

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+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+.Rproj.user
+inst/doc
+/doc/
+/Meta/
+docs
+
+# Annoying Rplot.pdf file that gets created while testing
+/tests/testthat/Rplots.pdf
+

BirdFlowExtras.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

DESCRIPTION

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+Package: BirdFlowExtras
+Type: Package
+Title: Extend BirdFlowR migration model functionality
+Version: 0.0.0.9001
+Authors@R: 
+    person("Ethan", "Plunkett",  email = "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0003-4405-2251"))
+Description: This includes functions that rely on BirdFlowR and a BirdFlow
+    model. They are in this second repository either because they are only 
+    likely to be useful to a subset of BirdFlowR users, or they depend on 
+    packages that are not on CRAN - in which case including them in BirdFlowR 
+    would make it CRAN incompatible. 
+    The initial motivation for a separate package was the calc_birdflow_mc()
+    function, but others will likely be added over time.
+License: MIT + file
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
+Suggests: 
+    BirdFlowModels,
+    spelling,
+    testthat (>= 3.0.0)
+Imports:
+    BirdFlowR,
+    MigConnectivity
+Remotes:
+    birdflow-science/BirdFlowModels,
+    birdflow-science/BirdFlowR,
+    SMBC-NZP/MigConnectivity
+URL: https://birdflow-science.github.io/BirdFlowExtras/, https://github.com/birdflow-science/BirdFlowExtras
+BugReports: https://github.com/birdflow-science/BirdFlowExtras/issue
+Language: en-US
+Depends: 
+    R (>= 3.5)
+Config/testthat/edition: 3

LICENSE.md

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+# MIT License
+
+Copyright (c) 2022 BirdFlowR authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(calc_birdflow_mc)
+import(BirdFlowR)

R/calc_birdflow_mc.R

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+#' Function to calculate migratory connectivity (MC) on a BirdFlow object
+#'
+#' This function calculates migratory connectivity based on the transitions
+#' in a BirdFlowR model using the raster cells as regions.
+#' It relies on `MigConnectivity::calcMC()` to do the bulk of the work.
+#'
+#' @param bf A BirdFlow model
+#' @inheritDotParams BirdFlowR::lookup_timestep_sequence -x
+#' @return The migratory connectivity of the BirdFlow model over the time period
+#' indicated by `...`
+#' @export
+#' @import BirdFlowR
+#' @examples
+#' bf <- BirdFlowModels::amewoo
+#' mc <- calc_birdflow_mc(bf, season = "prebreeding")
+#' print(mc)
+#'
+calc_birdflow_mc <- function(bf, ...) {
+
+  # Figure out time
+  ts <- lookup_timestep_sequence(bf, ...)
+  origin_t <- ts[1]
+  target_t <- ts[length(ts)]
+
+  # Dynamic masks
+  origin_dm <- get_dynamic_mask(bf, origin_t) # origin dynamic cells
+  target_dm <- get_dynamic_mask(bf, target_t) # target dynamic cells
+
+  # distance matricies
+  dist <- great_circle_distances(bf)  # all active cells
+  origin_dist <- dist[origin_dm, origin_dm] # origin dynamic
+  target_dist <- dist[target_dm, target_dm] # target dynamic
+
+  # Origin relative abundance
+  origin_abun <- get_distr(bf, origin_t)[origin_dm]
+
+  # Transition probabilities
+  psi <- t(combine_transitions(bf, ...))
+
+  # Double check dimensions
+  stopifnot(isTRUE(all.equal(nrow(psi), sum(origin_dm))))
+  stopifnot(isTRUE(all.equal(ncol(psi), sum(target_dm))))
+
+  # Calculate MC
+  mc <- MigConnectivity::calcMC(originDist = origin_dist,
+                                targetDist = target_dist,
+                                originRelAbund = origin_abun,
+                                psi = psi)
+
+  return(mc)
+}

README.Rmd

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+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+# BirdFlowExtras
+
+<!-- badges: start -->
+<!-- badges: end -->
+
+**BirdFlowExtras** extends **BirdFlowR** with functions that are anticipated to 
+be used by fewer users than the core functions; or that rely on packages that
+are not on CRAN or Bioconductor and thus cannot be used by packages on CRAN.
+
+## Installation
+
+You can install the development version of BirdFlowExtras like so:
+
+```r 
+if(!require("remotes"))
+  install.packages("remotes") 
+remotes::install_github("birdflow-science/BirdFlowR")
+```
+
+## Example
+
+Calculates Migratory Connectivity (MC) for a BirdFlowR model. This relies
+on the **MigConnectivity** package to do most of the work.
+
+```{r example}
+library(BirdFlowExtras)
+bf <- BirdFlowModels::amewoo
+calc_birdflow_mc(bf, season = "postbreeding")
+
+```
+

README.md

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+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# BirdFlowExtras
+
+<!-- badges: start -->
+<!-- badges: end -->
+
+**BirdFlowExtras** extends **BirdFlowR** with functions that are
+anticipated to be used by fewer users than the core functions; or that
+rely on packages that are not on CRAN or Bioconductor and thus cannot be
+used by packages on CRAN.
+
+## Installation
+
+You can install the development version of BirdFlowExtras like so:
+
+``` r
+if(!require("remotes"))
+  install.packages("remotes") 
+remotes::install_github("birdflow-science/BirdFlowR")
+```
+
+## Example
+
+Calculates Migratory Connectivity (MC) for a BirdFlowR model. This
+relies on the **MigConnectivity** package to do most of the work.
+
+``` r
+library(BirdFlowExtras)
+bf <- BirdFlowModels::amewoo
+calc_birdflow_mc(bf, season = "postbreeding")
+#> [1] 0.2690275
+```

inst/WORDLIST

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+BirdFlow
+BirdFlowR
+MigConnectivity
+timestep
+calc
+birdflow
+mc

tests/spelling.R

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+if (requireNamespace("spelling", quietly = TRUE))
+  spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                             skip_on_cran = TRUE)

tests/testthat.R

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+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(BirdFlowExtras)
+
+test_check("BirdFlowExtras")