diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 352481d..e93860d 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -24,17 +24,16 @@ jobs: env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 - uses: r-lib/actions/setup-r@v2 - uses: r-lib/actions/setup-tinytex@v2 - - name: Install dependencies - run: | - install.packages(c("remotes", "rcmdcheck")) - remotes::install_deps(dependencies = TRUE) - shell: Rscript {0} - - name: Check - run: | - options(crayon.enabled = TRUE) - rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error") - shell: Rscript {0} + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/DESCRIPTION b/DESCRIPTION index b80ddf7..1abec07 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -21,7 +21,7 @@ Depends: R (>= 3.6.0) License: GPL (>= 3) Encoding: UTF-8 LazyData: true -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 Imports: poems (>= 1.0.0), R6 (>= 2.5.0), @@ -33,7 +33,7 @@ Collate: PaleoPopResults.R PaleoRegion.R paleopop_simulator.R - paleopop.R + paleopop-package.R region_subset.R Suggests: testthat (>= 3.0.0), diff --git a/R/paleopop.R b/R/paleopop-package.R similarity index 98% rename from R/paleopop.R rename to R/paleopop-package.R index 2303eaa..00cfa65 100644 --- a/R/paleopop.R +++ b/R/paleopop-package.R @@ -1,3 +1,5 @@ +#' @keywords internal +"_PACKAGE" #' paleopop: Ensemble population modeling and simulation on paleo time scales #' #' The \code{paleopop} package is an extension of the \code{\link[poems:poems]{poems}} framework of \code{\link[R6:R6Class]{R6}} classes, which @@ -21,7 +23,6 @@ #' additional derived results. #' } #' -#' @docType package #' @name paleopop #' @importFrom utils read.csv read.table NULL \ No newline at end of file diff --git a/README.Rmd b/README.Rmd index 9ab7860..0de3154 100644 --- a/README.Rmd +++ b/README.Rmd @@ -13,13 +13,14 @@ knitr::opts_chunk$set( ) ``` -# paleopop +# paleopop - +[![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) `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. \ No newline at end of file diff --git a/cran-comments.md b/cran-comments.md index 8dede5b..488ebdb 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,9 +1,8 @@ # 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 @@ -11,16 +10,3 @@ # 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. \ No newline at end of file diff --git a/man/figures/logo.png b/man/figures/logo.png new file mode 100644 index 0000000..85407ce Binary files /dev/null and b/man/figures/logo.png differ diff --git a/man/paleopop-package.Rd b/man/paleopop-package.Rd new file mode 100644 index 0000000..c46b756 --- /dev/null +++ b/man/paleopop-package.Rd @@ -0,0 +1,31 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/paleopop-package.R +\docType{package} +\name{paleopop-package} +\alias{paleopop-package} +\title{paleopop: Pattern-Oriented Modeling Framework for Coupled Niche-Population Paleo-Climatic Models} +\description{ +\if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}} + +This extension of the poems pattern-oriented modeling (POM) framework provides a collection of modules and functions customized for paleontological time-scales, and optimized for single-generation transitions and large populations, across multiple generations. +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://github.com/GlobalEcologyLab/paleopop/} + \item Report bugs at \url{https://github.com/GlobalEcologyLab/paleopop/issues} +} + +} +\author{ +\strong{Maintainer}: July Pilowsky \email{pilowskyj@caryinstitute.org} (\href{https://orcid.org/0000-0002-6376-2585}{ORCID}) + +Authors: +\itemize{ + \item Sean Haythorne \email{sean.haythorne@adelaide.edu.au} + \item Stuart Brown \email{s.brown@adelaide.edu.au} (\href{https://orcid.org/0000-0002-0669-1418}{ORCID}) + \item Damien Fordham \email{damien.fordham@adelaide.edu.au} (\href{https://orcid.org/0000-0003-2137-5592}{ORCID}) +} + +} +\keyword{internal} diff --git a/man/paleopop.Rd b/man/paleopop.Rd index bc97eed..c15f3d6 100644 --- a/man/paleopop.Rd +++ b/man/paleopop.Rd @@ -1,6 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/paleopop.R -\docType{package} +% Please edit documentation in R/paleopop-package.R \name{paleopop} \alias{paleopop} \title{paleopop: Ensemble population modeling and simulation on paleo time scales}