Updated Github Actions

Github Actions have changed now that poems is back on CRAN. I've also prettied up the README file.

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

@@ -24,17 +24,16 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: r-lib/actions/setup-pandoc@v2
       - uses: r-lib/actions/setup-r@v2
       - uses: r-lib/actions/setup-tinytex@v2      
-      - name: Install dependencies
-        run: |
-          install.packages(c("remotes", "rcmdcheck"))
-          remotes::install_deps(dependencies = TRUE)
-        shell: Rscript {0}
-      - name: Check
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

DESCRIPTION

@@ -21,7 +21,7 @@ Depends: R (>= 3.6.0)
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Imports:
     poems (>= 1.0.0),
     R6 (>= 2.5.0),
@@ -33,7 +33,7 @@ Collate:
     PaleoPopResults.R
     PaleoRegion.R
     paleopop_simulator.R
-    paleopop.R
+    paleopop-package.R
     region_subset.R
 Suggests:
     testthat (>= 3.0.0),

R/paleopop.R → R/paleopop-package.R

@@ -1,3 +1,5 @@
+#' @keywords internal
+"_PACKAGE"
 #' paleopop: Ensemble population modeling and simulation on paleo time scales
 #'
 #' The \code{paleopop} package is an extension of the \code{\link[poems:poems]{poems}} framework of \code{\link[R6:R6Class]{R6}} classes, which 
@@ -21,7 +23,6 @@
 #'     additional derived results.
 #' }
 #' 
-#' @docType package
 #' @name paleopop
 #' @importFrom utils read.csv read.table
 NULL

README.Rmd

@@ -13,13 +13,14 @@ knitr::opts_chunk$set(
 )
 ```
 
-# paleopop
+# paleopop <img src='man/figures/logo.png' align="right" height="125" />
 
 <!-- badges: start -->
-
+[![Paper_doi](https://img.shields.io/badge/doi-10.1111/geb.13601-orange.svg)](https://doi.org/10.1111/geb.13601)
 [![R-CMD-check](https://github.com/GlobalEcologyLab/paleopop/workflows/R-CMD-check/badge.svg)](https://github.com/GlobalEcologyLab/paleopop/actions)
 [![CRAN status](https://www.r-pkg.org/badges/version/paleopop)](https://CRAN.R-project.org/package=paleopop)
 [![Download_count](https://cranlogs.r-pkg.org/badges/grand-total/paleopop)](https://CRAN.R-project.org/package=paleopop)
+[![Last commit](https://img.shields.io/github/last-commit/GlobalEcologyLab/paleopop.svg)](https://github.com/GlobalEcologyLab/paleopop/commits/master)
 <!-- badges: end -->
 
 `paleopop` is an extension to `poems`, a spatially-explicit, process-explicit, pattern-oriented framework for modeling population dynamics. This extension adds functionality for modeling large populations at generational time-steps over paleontological time-scales.
@@ -96,3 +97,9 @@ raster::plot(region$raster_from_values(results$abundance[,10]),
 ```
 
 A practical example of how to use `paleopop`, with more complex parameterization, can be found in the vignette.
+
+## Citation
+
+You may cite `paleopop` in publications using our software paper in *Global Ecology and Biogeography*:
+
+Pilowsky, J. A., Haythorne, S., Brown, S. C., Krapp, M., Armstrong, E., Brook, B. W., Rahbek, C., & Fordham, D. A. (2022). Range and extinction dynamics of the steppe bison in Siberia: A pattern‐oriented modelling approach. *Global Ecology and Biogeography*, *31*(12), 2483-2497.

cran-comments.md

@@ -1,26 +1,12 @@
 # Test environments
 
-- Local R 4.3.1 installation on Windows 10
-- Local R 4.3.1 installation on macOS 14.0 (intel chip)
+- Local R 4.4.1 installation on macOS 14.0 (intel chip)
 - Windows, R-devel (via win-builder)
-- Fedora Linux, R-devel (via r-hub)
+- Apple Silicon, R 4.4.1 (via mac-builder)
 
 # R CMD check results
 
 0 errors ✔ \| 0 warnings ✔ \| 1 note
 
 # Comments on check results
 
-> New submission
-  
-> Package was archived on CRAN
-  
-> Possibly misspelled words in DESCRIPTION:
-    Paleo (4:9)
-    paleontological (18:67)
-
-> CRAN repository db overrides:
-    X-CRAN-Comment: Archived on 2023-07-07 as requires archived package
-      'poems'.
-      
-      The words flagged as misspelled are common words in the field of paleo-ecology.