prioritizr · jeffreyhanson · Oct 7, 2024 · Oct 4, 2024 · Oct 4, 2024 · Oct 5, 2024
diff --git a/.github/workflows/R-CMD-check-ubuntu.yaml b/.github/workflows/R-CMD-check-ubuntu.yaml
@@ -24,9 +24,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: ubuntu-20.04, r: 'release'}
-          - {os: ubuntu-20.04, r: 'devel'}
-          - {os: ubuntu-20.04, r: 'devel', pkgs: 'depends only'}
+          - {os: ubuntu-22.04, r: 'release'}
+          - {os: ubuntu-22.04, r: 'devel'}
+          - {os: ubuntu-22.04, r: 'devel', pkgs: 'depends only'}
 
     env:
       _R_REMOTES_NO_ERRORS_FROM_WARNINGS_: true

diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml
@@ -24,7 +24,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: ubuntu-20.04, r: 'release', pkgs: 'all'}
+          - {os: ubuntu-22.04, r: 'release', pkgs: 'all'}
 
     env:
       _R_REMOTES_NO_ERRORS_FROM_WARNINGS_: true
@@ -83,9 +83,9 @@ jobs:
       - name: Check URLs
         if: runner.os == 'Linux' && matrix.config.r == 'release'
         run: |
+          d <- suppressWarnings(readLines("inst/URLLIST"))
           result <- urlchecker::url_check()
-          result <- result[!startsWith(result$URL, "https://doi.org/"), , drop = FALSE]
-          result <- result[!startsWith(result$URL, "http://geo.abds.is"), , drop = FALSE]
+          result <- result[!result$URL %in% d, , drop = FALSE]
           if (nrow(result) > 0) {
             print(result)
             stop("Invalid URLs detected")

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: wdpar
 Type: Package
-Version: 1.3.7.4
+Version: 1.3.8
 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
@@ -45,7 +45,7 @@ Language: en-US
 URL: https://prioritizr.github.io/wdpar/, https://github.com/prioritizr/wdpar
 BugReports: https://github.com/prioritizr/wdpar/issues
 VignetteBuilder: knitr
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Collate:
     'internal.R'
     'package.R'

diff --git a/NEWS.md b/NEWS.md
@@ -1,16 +1,21 @@
+# wdpar 1.3.8
+
+- CRAN release.
+- Minor improvements to documentation.
+
 # wdpar 1.3.7.4
 
 - Fix typo in text formatting for `wdpa_clean()` documentation.
 
 # wdpar 1.3.7.3
 
-- Fix issues with `wdpa_fetch()` and `wdpa_read()` on MacOS.
+- Fix bugs in `wdpa_fetch()` and `wdpa_read()` on MacOS.
   Thanks to Jason Everett (@jaseeverett) for code contribution.
 - Update DESCRIPTION with _prepr_ package information.
 - Update README with Chromium dependencies.
 - Update global example global processing script with increased precision.
 - Update vignette to be compatible with changes to GADM website.
-- Fix issue with tests leaving left-over junk in temporary directories.
+- Fix issue with tests leaving left-over files in temporary directories.
 
 # wdpar 1.3.7.2
 
@@ -26,7 +31,6 @@
   characters from the `"MANG_PLAN"` field.
 - Fix bug in `wdpa_read()` that causes output objects to contain no columns.
 - Update README and vignette to be compatible with updates to _ggmap_ package.
-- Remove _withr_ package from DESCRIPTION because it is not used.
 
 # wdpar 1.3.7.1
 

diff --git a/R/read_sf_n.R b/R/read_sf_n.R
@@ -10,7 +10,7 @@
 #' @param n `integer` number of records to import.
 #'   Defaults to `NULL` such that all data are imported.
 #'
-#' @return [sf::sf()] object.
+#' @return A [sf::sf()] object.
 #'
 #' @noRd
 read_sf_n <- function(dsn, layer = NULL, n = NULL) {

diff --git a/R/st_erase_overlaps.R b/R/st_erase_overlaps.R
@@ -13,7 +13,7 @@ NULL
 #' @details This is a more robust -- albeit slower -- implementation for
 #'   [sf::st_difference()] when `y` is missing.
 #'
-#' @return [sf::sf()] object.
+#' @return A [sf::sf()] object.
 #'
 #' @seealso [sf::st_difference()], [wdpa_dissolve()].
 #'

diff --git a/R/st_repair_geometry.R b/R/st_repair_geometry.R
@@ -30,6 +30,8 @@
 #' installed before the package itself can be installed
 #' (see package README file for platform-specific instructions).
 #'
+#' @return A [sf::sf()] object.
+#'
 #' @examples
 #' # create sf object
 #' p1 <- st_sf(
@@ -42,6 +44,7 @@
 #'
 #' # print object
 #' print(p2)
+#"
 #' @export
 st_repair_geometry <- function(x, geometry_precision = 1500) {
   # assert arguments are valid

diff --git a/R/wdpa_clean.R b/R/wdpa_clean.R
@@ -181,7 +181,7 @@ NULL
 #' For an example of processing a large protected area dataset,
 #' please see the vignette.
 #'
-#' @return [sf::sf()] object.
+#' @return A [sf::sf()] object.
 #'
 #' @seealso [wdpa_fetch()], [wdpa_dissolve()].
 #'

diff --git a/R/wdpa_fetch.R b/R/wdpa_fetch.R
@@ -93,13 +93,13 @@ NULL
 #' you can assume that the function still worked correctly.
 #' For reference, the misleading message will look something like this:
 #' ```
-#' [2024-04-23 12:06:36] [error] handle_read_frame error: websocketpp.transport:7 (End of File)
+#' [error] handle_read_frame error: websocketpp.transport:7 (End of File)
 #' ```
 #'
 #' For further help with troubleshooting, please refer to the documentation
 #' for the \pkg{chromote} package (https://rstudio.github.io/chromote/).
 #'
-#' @return [sf::sf()] object.
+#' @return A [sf::sf()] object.
 #'
 #' @seealso [wdpa_clean()], [wdpa_read()],
 #'   [wdpa_url()], [countrycode::countrycode()].

diff --git a/R/wdpa_latest_version.R b/R/wdpa_latest_version.R
@@ -14,7 +14,7 @@ NULL
 #'   global dataset is available. For specific details, please refer to
 #'   the source code for this function.
 #'
-#' @return `character` version of the dataset.
+#' @return A `character` value with the dataset version.
 #'
 #' @examples
 #' \dontrun{

diff --git a/R/wdpa_read.R b/R/wdpa_read.R
@@ -24,7 +24,7 @@ NULL
 #'
 #' @inheritSection wdpa_fetch Data source
 #'
-#' @return [sf::sf()] object.
+#' @return A [sf::sf()] object.
 #'
 #' @seealso [wdpa_fetch()], [wdpa_clean()].
 #'

diff --git a/R/wdpa_url.R b/R/wdpa_url.R
@@ -39,7 +39,7 @@ NULL
 #'   and (`"gdb"`) file geodatabase format. Defaults to `"gdb".
 #'   Note that global data are only available in file geodatabase format.
 #'
-#' @return `character` URL to download the data.
+#' @return A `character` value with the URL to download the data.
 #'
 #' @seealso [wdpa_fetch()], [countrycode::countrycode()].
 #'

diff --git a/README.Rmd b/README.Rmd
@@ -126,7 +126,7 @@ Print preview of the data associated with each protected area.
 head(mlt_pa_data)
 ```
 
-Finally, after cleaning the data, let's plot a map showing Malta's protected areas and color each area according to its management category ([as defined by the The International Union for Conservation of Nature](https://www.iucn.org/)).
+Finally, after cleaning the data, let's plot a map showing Malta's protected areas and color each area according to its management category ([as defined by the The International Union for Conservation of Nature](https://iucn.org/)).
 
 ```{r "readme-map", message = FALSE, warning = FALSE, out.width = ifelse(isTRUE(knitr:::is_html_output(excludes = c("markdown"))), "60%", "50%")}
 # reproject data to longitude/latitude for plotting

diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@
 [![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://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)
+[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/wdpar)](https://CRAN.R-project.org/package=wdpar)
 
 ### Overview
 
@@ -114,8 +114,8 @@ installed using the following system commands:
 ##### *Linux*
 
 For Unix-alikes, a Chromium-based web browser (e.g., Google Chrome,
-Chromium, Brave), `gmp` (&gt;= 4.2.3), `mpfr` (&gt;= 3.0.0), and `gdal`
-(&gt;= 3.2.2) are required.
+Chromium, Brave), `gmp` (\>= 4.2.3), `mpfr` (\>= 3.0.0), and `gdal` (\>=
+3.2.2) are required.
 
 ##### *macOS*
 
@@ -184,18 +184,18 @@ head(mlt_pa_data)
     ## Simple feature collection with 6 features and 32 fields
     ## Geometry type: MULTIPOLYGON
     ## Dimension:     XY
-    ## Bounding box:  xmin: 1382584 ymin: 4280853 xmax: 1390560 ymax: 4299615
+    ## Bounding box:  xmin: 1382584 ymin: 4280853 xmax: 1394227 ymax: 4299615
     ## Projected CRS: +proj=cea +lon_0=0 +lat_ts=30 +x_0=0 +y_0=0 +datum=WGS84 +ellps=WGS84 +units=m +no_defs
     ## Precision:     1500 
     ## # A tibble: 6 × 33
     ##      WDPAID WDPA_PID  PA_DEF NAME  ORIG_NAME DESIG DESIG_ENG DESIG_TYPE IUCN_CAT
     ##       <dbl> <chr>     <chr>  <chr> <chr>     <chr> <chr>     <chr>      <chr>   
-    ## 1    194425 194425    PA     'Il-… 'Il-Gżej… Rise… Nature R… National   Ia      
+    ## 1    194425 194425    PA     Il-G… Il-Gżejj… Rise… Nature R… National   Ia      
     ## 2    194420 194420    PA     Filf… Filfla    Rise… Nature R… National   Ia      
-    ## 3 555588631 555588631 PA     Il-M… Il-Majji… Park… National… National   II      
-    ## 4    174758 174758    PA     Bidn… Bidnija,… List… List of … National   III     
+    ## 3 555700375 555700375 PA     Il-P… Il-Ponta… Rise… Nature R… National   Ia      
+    ## 4 555588631 555588631 PA     Il-M… Il-Majji… Park… National… National   II      
     ## 5    194418 194418    PA     Il-B… Il-Ballu… List… List of … National   III     
-    ## 6    194417 194417    PA     'Il-… 'Il-Wied… List… List of … National   III     
+    ## 6    194415 194415    PA     Il-Ġ… Il-Ġonna… List… List of … National   III     
     ## # ℹ 24 more variables: INT_CRIT <chr>, MARINE <chr>, REP_M_AREA <dbl>,
     ## #   GIS_M_AREA <dbl>, REP_AREA <dbl>, GIS_AREA <dbl>, NO_TAKE <chr>,
     ## #   NO_TK_AREA <dbl>, STATUS <chr>, STATUS_YR <dbl>, GOV_TYPE <chr>,
@@ -207,7 +207,7 @@ head(mlt_pa_data)
 Finally, after cleaning the data, let’s plot a map showing Malta’s
 protected areas and color each area according to its management category
 ([as defined by the The International Union for Conservation of
-Nature](https://www.iucn.org/)).
+Nature](https://iucn.org/)).
 
 ``` r
 # reproject data to longitude/latitude for plotting

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -3,6 +3,7 @@ authors:
     href: http://jeffrey-hanson.com
 
 template:
+  bootstrap: 5
   params:
     bootswatch: flatly
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,15 +1,15 @@
 Dear CRAN volunteers,
 
-Thank you for reviewing this submission. The main updates in this version include (i) a bug fix for the data cleaning procedures and (ii) fixing the alias for package-level documentation.
+Thank you for reviewing this submission. It contains an update to the _wdpar_ package that has been on CRAN since 2019. The main changes in this new version include (i) updates to maintain compatibility with the Protected Planet website and the World Database on Protected Areas, (ii) functionality to download data in different file formats, (iii) bug fixes to address issues on MacOS systems, and (iv) assorted improvements to the documentation.
 
 Cheers,
 
 Jeff
 
 # Test environments
 
-* [Ubuntu 20.04, R-release](https://github.com/prioritizr/wdpar/actions?query=workflow%3AUbuntu)
-* [Ubuntu 20.04, R-devel](https://github.com/prioritizr/wdpar/actions?query=workflow%3AUbuntu)
+* [Ubuntu 22.04, R-release](https://github.com/prioritizr/wdpar/actions?query=workflow%3AUbuntu)
+* [Ubuntu 22.04, R-devel](https://github.com/prioritizr/wdpar/actions?query=workflow%3AUbuntu)
 * [Mac OSX 10.15, R-release](https://github.com/prioritizr/wdpar/actions?query=workflow%3A%22Mac+OSX%22)
 * [macOS 11.5.2 (arm64), R-release (macOS builder)](https://mac.r-project.org/macbuilder/submit.html)
 * [Windows Server 2019, R-release](https://github.com/prioritizr/wdpar/actions?query=workflow%3AWindows)
@@ -29,7 +29,7 @@ Jeff
 * Suggests or Enhances not in mainstream repositories:
   prepr
 
-  **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.**
+  **The prepr R package is an optional dependency that is available on GitHub (<https://github.com/prioritizr/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