update citation (#66)

* update citation * rebuild site * update urls + cran comments
prioritizr · Feb 24, 2023 · d4c52e4 · d4c52e4
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,13 +1,14 @@
 Package: wdpar
 Type: Package
-Version: 1.3.3.6
+Version: 1.3.4
 Title: Interface to the World Database on Protected Areas
 Description: Fetch and clean data from the World Database on Protected
     Areas (WDPA) and the World Database on Other Effective Area-Based
     Conservation Measures (WDOECM). Data is obtained from Protected Planet
     <https://www.protectedplanet.net/en>. To augment data cleaning procedures,
     users can install the 'prepr' R package (available at
-    <https://github.com/dickoa/prepr>).
+    <https://github.com/dickoa/prepr>). For more information on this package,
+    see Hanson (2022) <doi:10.21105/joss.04594>.
 Authors@R: c(person(c('Jeffrey', 'O'), 'Hanson',
     email='jeffrey.hanson@uqconnect.edu.au', role = c('aut', 'cre')))
 Imports:

diff --git a/Makefile b/Makefile
@@ -46,6 +46,9 @@ wbcheck:
 solarischeck:
 	R --slave -e "rhub::check(platform = 'solaris-x86-patched', email = 'jeffrey.hanson@uqconnect.edu.au', show_status = FALSE)"
 
+maccheck:
+	R --slave -e "devtools::check_mac_release()"
+
 build:
 	R --slave -e "devtools::build()"
 	cp -R doc inst/

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# wdpar 1.3.4
+
+- CRAN release.
+- Update citation format.
+
 # wdpar 1.3.3.6
 
 - Fix broken URL in vignette.

diff --git a/README.Rmd b/README.Rmd
@@ -18,54 +18,13 @@ knitr::opts_chunk$set(fig.path = "man/figures/README-", fig.align = "center",
 [![R-CMD-check-Windows](https://img.shields.io/github/actions/workflow/status/prioritizr/wdpar/R-CMD-check-windows.yaml?branch=master&label=Windows)](https://github.com/prioritizr/wdpar/actions)
 [![R-CMD-check-macOS](https://img.shields.io/github/actions/workflow/status/prioritizr/wdpar/R-CMD-check-macos.yaml?branch=master&label=macOS)](https://github.com/prioritizr/wdpar/actions)
 [![Documentation](https://img.shields.io/github/actions/workflow/status/prioritizr/wdpar/documentation.yaml?branch=master&label=Documentation)](https://github.com/prioritizr/wdpar/actions)
-[![Coverage Status](https://img.shields.io/codecov/c/github/prioritizr/wdpar?label=Coverage)](https://codecov.io/github/prioritizr/wdpar?branch=master)
+[![Coverage Status](https://img.shields.io/codecov/c/github/prioritizr/wdpar?label=Coverage)](https://app.codecov.io/gh/prioritizr/wdpar/branch/master)
 [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/wdpar)](https://CRAN.R-project.org/package=wdpar)
 
 ```{r, include = FALSE}
 devtools::load_all()
 ```
 
-```{r, include = FALSE}
-# define helpers
-is_rel_version <- function(x) {
-  length(strsplit(as.character(x), ".", fixed = TRUE)[[1]]) == 3
-}
-
-package_version_year <- function(x) {
-  if (x %in% rownames(available.packages())) {
-    return(live_package_version_year(x))
-  } else {
-    return(archive_package_version_year(x))
-  }
-}
-
-live_package_version_year <- function(x) {
-  # fetch data
-  d <- versions::available.versions(x)[[1]]
-  d <- d[which(d$version == max(d$version)), , drop = FALSE]
-  c(as.character(d$version), as.character(format(as.POSIXct(d$date), "%Y")))
-}
-
-archive_package_version_year <- function(x) {
-  # fetch data (copied from remotes R package)
-  tf <- tempfile(fileext = ".gz")
-  on.exit(unlink(tf), add = TRUE)
-  download.file(tf, url = sprintf("%s/src/contrib/Meta/archive.rds", repo))
-  con <- gzfile(tf, "rb")
-  on.exit(close(con), add = TRUE)
-  d <- readRDS(con)[[x]]
-  # extract version
-  rel_version <- basename(rownames(d))
-  rel_version <- sapply(strsplit(rel_version, "_", fixed = TRUE), `[[`, 2)
-  rel_version <- sapply(strsplit(rel_version, ".tar", fixed = TRUE), `[[`, 1)
-  rel_version <- max(rel_version)
-  # extract year
-  rel_year <- as.character(max(format(d[, "mtime"], "%Y")))
-  # return year version
-  c(rel_version, rel_year)
-}
-```
-
 ### Overview
 
 [Protected Planet](https://www.protectedplanet.net/en) provides the most comprehensive data for conservation areas worldwide. Specifically, it provides the World Database on Protected Areas (WDPA) and the World Database on Other Effective Area-Based Conservation Measures (WDOECM). These databases are used to monitor the performance of existing protected areas, and identify priority areas for future conservation efforts. Additionally, these databases receive monthly updates from government agencies and non-governmental organizations. However, they are associated with [several issues that need to be addressed prior to analysis](https://www.protectedplanet.net/en/resources/calculating-protected-area-coverage) and the dynamic nature of these databases means that the entire data cleaning process needs to be repeated after obtaining a new version.
@@ -188,18 +147,6 @@ If you need to calculate protected area coverage statistics for a country, pleas
 
 ### Citation
 
-```{r, include = FALSE}
-dev_version_year <- c(
-  as.character(packageDescription("wdpar")$Version),
-  format(Sys.time(), "%Y")
-)
-if (is_rel_version(dev_version_year[[1]])) {
-  rel_version_year <- dev_version_year
-} else {
-  rel_version_year <- package_version_year("wdpar")
-}
-```
-
 Please cite the _wdpar R_ package and the relevant databases used in publications.
 
 To cite the package, please use:

diff --git a/README.md b/README.md
@@ -9,7 +9,7 @@
 [![R-CMD-check-macOS](https://img.shields.io/github/actions/workflow/status/prioritizr/wdpar/R-CMD-check-macos.yaml?branch=master&label=macOS)](https://github.com/prioritizr/wdpar/actions)
 [![Documentation](https://img.shields.io/github/actions/workflow/status/prioritizr/wdpar/documentation.yaml?branch=master&label=Documentation)](https://github.com/prioritizr/wdpar/actions)
 [![Coverage
-Status](https://img.shields.io/codecov/c/github/prioritizr/wdpar?label=Coverage)](https://codecov.io/github/prioritizr/wdpar?branch=master)
+Status](https://img.shields.io/codecov/c/github/prioritizr/wdpar?label=Coverage)](https://app.codecov.io/gh/prioritizr/wdpar/branch/master)
 [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/wdpar)](https://CRAN.R-project.org/package=wdpar)
 
 ### Overview

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,6 +1,6 @@
 Dear CRAN volunteers,
 
-Thank you for reviewing this submission. The main updates in this version include (i) making data download procedures more robust, (ii) fixing compatibility issues with recent updates to GEOS (version 3.11.0), (iii) improving the documentation.
+Thank you for reviewing this submission. The main updates in this version include (i) making data download and cleaning procedures more robust, (ii) improving the documentation, and (iii) updating the citation information.
 
 Cheers,
 
@@ -17,7 +17,7 @@ Jeff
 
 # R CMD check results
 
-0 errors | 0 warnings | 2 note
+0 errors | 0 warnings | 3 notes
 
 # Package check notes
 
@@ -31,6 +31,18 @@ Jeff
 
   **The prepr R package is an optional dependency that is available on GitHub (<https://github.com/dickoa/prepr>). Instructions for installing the prepr R package are provided in the DESCRIPTION file and the package README file.**
 
+* Found the following (possibly) invalid URLs:
+    URL: https://doi.org/10.1111/conl.12158
+      FROM: README.md
+      Status: Service Unavailable
+      Message: 503
+    URL: https://doi.org/10.1126/science.aac9180
+      FROM: README.md
+      Status: Service Unavailable
+      Message: 503
+
+  **I have manually checked and can confirm that these URLs are correct.**
+
 # Downstream dependencies
 
 There are no existing packages that depend on this package.
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/wdpar.html b/docs/articles/wdpar.html
diff --git a/docs/authors.html b/docs/authors.html