update data, add basic tests

Data updated through Nov 2023

Author: ericward-noaa

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,58 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: rcmdcheck
+
+      - uses: r-lib/actions/check-r-package@v2
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

DESCRIPTION

@@ -1,20 +1,22 @@
 Package: kwdemog
 Type: Package
 Title: Package for processing and exploring killer whale demographic data
-Version: 1.0.2
-Date: 2021-12-12
+Version: 1.0.3
+Date: 2023-12-15
 Authors@R: c(
     person(c("Eric", "J."), "Ward", email = "eric.ward@noaa.gov", 
       role = c("aut", "cre")))
 Description: Generates killer whale demographic data from rows (observations) and fits preliminary models.
 Depends:
     R (>= 4.0.0)
-Imports: dplyr,ggplot2,mgcv,usethis,rstanarm,stringr,viridis,ggridges
+Imports: dplyr,mgcv,usethis,stringr,ggridges,ggplot2,rstanarm,viridis
 Suggests: knitr,
     rmarkdown,
     gridExtra
+URL: https://noaa-nwfsc.github.io/srkw-status/
+BugReports: https://github.com/noaa-nwfsc/srkw-status/issues
 License: GPL (>=3)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Encoding: UTF-8
 VignetteBuilder: knitr
 LazyData: true

LICENSE

@@ -5,6 +5,7 @@ export(project)
 export(writedata)
 import(dplyr)
 import(mgcv)
+importFrom(stats,rbeta)
 importFrom(stats,rnorm)
 importFrom(stats,runif)
 importFrom(stringr,str_locate)

NAMESPACE

@@ -24,8 +24,8 @@ expand <- function(filename, start_year = 1976, current_year = NULL,
   fem_age_mat = 10, fem_age_senesc = 43, ages2stages = NULL) {
   if(is.null(current_year)) current_year = as.numeric(substr(Sys.Date(),1,4))
 
-  if(class(filename) == "data.frame") orca = filename
-  if(class(filename) == "character") orca = read.csv(filename, stringsAsFactors = FALSE)
+  if(inherits(filename, "data.frame")) orca = filename
+  if(inherits(filename, "character")) orca = read.csv(filename, stringsAsFactors = FALSE)
   orca$population = ifelse(orca$pod %in% c("J001","K001","L001"), "SRKW", "NRKW")
   # create expanded data frame of all years and animals
   alldat = expand.grid("year" = start_year:current_year,

R/expand.R

@@ -9,15 +9,12 @@
 #' e.g. "1981:1985" to use rates from 1981 to 1985 or ("1981:1985","1981:2021")
 #' @param verbose whether to print status updates to screen, defaults to FALSE
 #' @param p_female The probability of a female birth, defaults to the empirical value since 1980
-#' @param n_births Used for uncertainty in the sex ratio at birth. The distribution of female births is 
-#' assumed to be beta binomial, with shape parameters `(n_births+1)*p_female` and `(n_births+1)*(1-p_female)`.
-#' There have been approximately 100 births since 1980, and this defaults to the empirical number
-#' of births
-#' formula above
+#' @param n_births The number of births used to calculate `p_female`. By default, this defaults to the empirical
+#' value observed since 1980 the probability of female birth. Larger values result in more precise estimates of `p_female`
 #' 
 #' @import dplyr
 #' @import mgcv
-#' @importFrom stats rnorm runif
+#' @importFrom stats rnorm runif rbeta
 #' @importFrom stringr str_locate
 #'
 #' @export
@@ -27,7 +24,7 @@ project = function(whale_data, seed = 123,
                       n_iter = 200, 
                       verbose = FALSE,
                       p_female = NA,
-                      sd_female = NA) {
+                      n_births = NA) {
   set.seed(seed)
 
   data = whale_data
@@ -101,7 +98,8 @@ project = function(whale_data, seed = 123,
 
       initPopCurrent$sex = as.numeric(initPopCurrent$sex)
       # assign sexes to unsexed individuals [0s]
-      initPopCurrent$sex[which(initPopCurrent$Sex==0)] = ifelse(runif(length(which(initPopCurrent$sex==0))) < rnorm(length(which(initPopCurrent$sex==0)),p_female, sd_female), 1, 2)
+      initPopCurrent$sex[which(initPopCurrent$Sex==0)] = ifelse(runif(length(which(initPopCurrent$sex==0))) < rbeta(length(which(initPopCurrent$sex==0)), beta_1, beta_2), 1, 2)
+      #initPopCurrent$sex[which(initPopCurrent$Sex==0)] = ifelse(runif(length(which(initPopCurrent$sex==0))) < rnorm(length(which(initPopCurrent$sex==0)),p_female, sd_female), 1, 2)
       newID = 9999
 
       for(yrs in 1:dim(popSize)[2]) {

R/project.R

@@ -1,6 +1,6 @@
 # 'kwdemog' package  
 
-This is a repository (pkgdown site here: https://nwfsc-cb.github.io/srkw-status/) for archiving code and data related to projecting Southern Resident killer whale population status. The data are included as an .rda file in the /data folder. In addition to using this framework for population projections this has been used extensively for the Pacific Fishery Management Council Working Group to understand the effects of ocean salmon fisheries on killer whales. 
+This is a repository (pkgdown site here: https://noaa-nwfsc.github.io/srkw-status/) for archiving code and data related to projecting Southern Resident killer whale population status. The data are included as an .rda file in the /data folder. In addition to using this framework for population projections this has been used extensively for the Pacific Fishery Management Council Working Group to understand the effects of ocean salmon fisheries on killer whales. 
 
 [2020 PFMC Risk Assessment](https://www.pcouncil.org/documents/2020/02/e-3-a-srkw-workgroup-report-1-electronic-only.pdf/)