misc fixes (#51)

- Remove rgdal package dependency - Updates URLs - Update functions for downloading preprocessed data from Zenodo - Update plotting functions to handle changes to ggmap
prioritizr · Nov 2, 2023 · 34ae091 · 34ae091
1 parent 85bdd0c
commit 34ae091
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diff --git a/.github/workflows/R-CMD-check-macos.yaml b/.github/workflows/R-CMD-check-macos.yaml
@@ -71,7 +71,6 @@ jobs:
           install.packages("sf")
           install.packages("terra")
           install.packages("lwgeom")
-          install.packages("rgdal")
           remotes::install_github("dickoa/prepr")
           remotes::install_github("r-spatial/link2GI")
         shell: Rscript {0}
@@ -83,6 +82,11 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
+      - name: Set R environmental variables
+        run: |
+          echo GGMAP_STADIAMAPS_API_KEY="$GGMAP_KEY" >> ~/.Renviron
+        shell: bash
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true

diff --git a/.github/workflows/R-CMD-check-ubuntu.yaml b/.github/workflows/R-CMD-check-ubuntu.yaml
@@ -34,6 +34,7 @@ jobs:
       _R_CHECK_TIMINGS_: 10
       _R_CHECK_CRAN_INCOMING_REMOTE_: false
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      GGMAP_KEY: ${{ secrets.GGMAP_STADIAMAPS_API_KEY }}
       CI: true
 
     steps:
@@ -76,7 +77,6 @@ jobs:
       - name: Install spatial R packages
         run: |
           options(repos = "https://cloud.r-project.org/")
-          install.packages("rgdal")
           install.packages("sf")
           install.packages("terra")
           install.packages("lwgeom")
@@ -93,6 +93,11 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
+      - name: Set R environmental variables
+        run: |
+          echo GGMAP_STADIAMAPS_API_KEY="$GGMAP_KEY" >> ~/.Renviron
+        shell: bash
+
       - name: Environmental variables
         if: matrix.config.pkgs == 'depends only'
         run: |

diff --git a/.github/workflows/R-CMD-check-windows.yaml b/.github/workflows/R-CMD-check-windows.yaml
@@ -69,7 +69,6 @@ jobs:
           install.packages("sf")
           install.packages("terra")
           install.packages("lwgeom")
-          install.packages("rgdal")
           remotes::install_github("dickoa/prepr")
         shell: Rscript {0}
 
@@ -80,6 +79,11 @@ jobs:
           sessioninfo::session_info(pkgs, include_base = TRUE)
         shell: Rscript {0}
 
+      - name: Set R environmental variables
+        run: |
+          echo GGMAP_STADIAMAPS_API_KEY="$GGMAP_KEY" >> ~/.Renviron
+        shell: bash
+
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true

diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml
@@ -73,7 +73,6 @@ jobs:
       - name: Install spatial R packages
         run: |
           options(repos = "https://cloud.r-project.org/")
-          install.packages("rgdal")
           install.packages("sf")
           install.packages("terra")
           install.packages("lwgeom")

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: aoh
 Type: Package
-Version: 0.0.2.8
+Version: 0.0.2.9
 Title: Create Area of Habitat Data
 Description: Create Area of Habitat data to characterize species distributions.
     Data are produced following procedures outlined by Brooks et al. (2019)
@@ -42,19 +42,19 @@ Imports:
     ggplot2 (>= 3.1.0),
     fasterize (>= 1.0.3),
     raster (>= 3.5-15),
-    rvest (>= 1.0.3)
+    rvest (>= 1.0.3),
+    jsonlite (>= 1.8.7)
 Suggests:
     sp (>= 2.0.0),
     testthat (>= 2.0.1),
     knitr (>= 1.2.0),
     roxygen2 (>= 6.1.1),
     rmarkdown (>= 1.10),
     pingr (>= 1.1.2),
-    ggmap (>= 2.6.1),
+    ggmap (>= 3.0.2.9002),
     fields (>= 14.0),
     smoothr (>= 0.2.2),
     rnaturalearth (>= 0.3.3),
-    rgdal (>= 1.5.27),
     gdalUtilities (>= 1.2.1),
     archive (>= 1.1.2),
     link2GI (>= 0.5-0),
@@ -132,4 +132,5 @@ Collate:
 Roxygen: list(markdown = TRUE)
 Remotes:
   dickoa/prepr,
-  r-spatial/link2GI
+  r-spatial/link2GI,
+  dkahle/ggmap
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,11 @@
+# aoh 0.0.2.9
+
+- Remove _rgdal_ package dependency.
+- Updates URLs.
+- Update functions for downloading preprocessed data from Zenodo.
+- Update `plot_spp_aoh_data()` and `plot_spp_frc_data()` to be compatible
+  with changes to the _ggmap_ package for creating maps with a basemap.
+
 # aoh 0.0.2.8
 
 - Fix failing tests on continuous integration services (due to issues unzipping

diff --git a/R/misc_zenodo.R b/R/misc_zenodo.R
@@ -34,19 +34,14 @@ get_doi_files <- function(x) {
   # scrape html file
   d <- rvest::read_html(x)
 
-  # find file container
-  file_div <- rvest::html_elements(d, css = ".files-box")
-
-  # find table in file container
-  file_table <- rvest::html_element(file_div, "table")
-  file_rows <- rvest::html_children(rvest::html_element(file_table, "tbody"))
-  file_info <- rvest::html_element(file_rows, "a")
+  # extract metedata
+  md <- rvest::html_elements(d, css = "#recordVersions")
+  md <- jsonlite::fromJSON(rvest::html_attr(md, "data-record"))
 
   # extract file details
-  file_names <- rvest::html_text(file_info)
-  file_urls <- paste0(
-    "https://zenodo.org", rvest::html_attr(file_info, "href")
-  )
+  file_names <- names(md$files$entries)
+  file_urls <- paste0(md$links$files, "/", file_names, "?download=1")
+  file_urls <- gsub("/api/", "/", file_urls, fixed = TRUE)
 
   # return result
   tibble::tibble(filename = file_names, download = file_urls)
@@ -83,53 +78,35 @@ get_doi_versions <- function(x) {
   d <- rvest::read_html(x)
 
   # find metadata containers
-  metadata_divs <- rvest::html_elements(d, css = ".metadata")
-
-  # extract div containing version numbers
-  is_version_div <- vapply(metadata_divs, FUN.VALUE = logical(1), function(x) {
-    h <- rvest::html_elements(x, css = "h4")
-    if (length(h) == 0) return(FALSE)
-    h <- h[[1]]
-    identical(rvest::html_text(h), "Versions")
+  md <- rvest::html_elements(d, css = "#recordVersions")
+  md <- jsonlite::fromJSON(rvest::html_attr(md, "data-record"))
+  md <- rvest::read_html(md$links$versions)
+  md <- jsonlite::fromJSON(rvest::html_text(md), "p")$hits[[1]]
+
+  # extract metadata
+  version <- vapply(md, FUN.VALUE = character(1), function(x) {
+    if (is.null(x$metadata)) return(NA_character_)
+    if (is.null(x$metadata$version)) return(NA_character_)
+    trimws(x$metadata$version)
   })
-
-  # return input doi if it's not associated with any versions
-  if (!any(is_version_div)) {
-    d <- tibble::tibble(
-      version = NA_character_,
-      created = as.POSIXct(NA_real_),
-      doi = gsub("https://doi.org/", "", x, fixed = TRUE)
-    )
-    return(d)
-  }
-
-  # extract div containing version numbers
-  version_div <- metadata_divs[[which(is_version_div)[[1]]]]
-
-  # extract version table
-  version_table <- rvest::html_element(version_div, "table")
-  version_rows <- rvest::html_children(version_table)
-
-  # parse information for each version
-  info <- lapply(version_rows, function(x) {
-    tibble::tibble(
-      version = trimws(gsub(
-        "Version ", "", fixed = TRUE,
-        rvest::html_text(rvest::html_element(x, "a"))
-      )),
-      created = as.POSIXct(
-        trimws(rvest::html_text(
-          rvest::html_element(rvest::html_children(x)[[2]], "small")
-        )),
-        format = "%b %e, %Y"
-      ),
-      doi = trimws(rvest::html_text(rvest::html_element(x, "small"))),
-    )
+  created <- vapply(md, FUN.VALUE = character(1), function(x) {
+    if (is.null(x$metadata)) return(NA_character_)
+    if (is.null(x$metadata$publication_date)) return(NA_character_)
+    trimws(x$metadata$publication_date)
+  })
+  doi <- vapply(md, FUN.VALUE = character(1), function(x) {
+    if (is.null(x$metadata)) return(NA_character_)
+    if (is.null(x$metadata$doi)) return(NA_character_)
+    trimws(x$metadata$doi)
   })
 
-  # compile table
-  info <- dplyr::bind_rows(info)
+  # create table with metadata
+  info <- tibble::tibble(
+    version = version,
+    created = as.POSIXct(created, format = "%Y-%m-%d"),
+    doi = doi
+  )
 
-  ## return result (reverse row ordering for compatibility with zen4R
+  # return result (reverse row ordering for compatibility with zen4R
   info[rev(seq_len(nrow(info))), , drop = FALSE]
 }
diff --git a/R/plot_spp_aoh_data.R b/R/plot_spp_aoh_data.R
@@ -18,22 +18,22 @@ NULL
 #'   spatial extent of the data.
 #'
 #' @param zoom `numeric` Value indicating the zoom level for the basemap.
-#'   See documentation for the `zoom` parameter in the [ggmap::get_stamenmap()]
+#'   See documentation for the `zoom` parameter in the [ggmap::get_stadiamap()]
 #'   function for details.
 #'   Defaults to `NULL` such that no basemap is shown.
 #'
 #' @param maptype `character` Value indicating the name of the
 #'   the basemap to use for the plot.
 #'   See documentation for the `maptype` parameter in the
-#'   [ggmap::get_stamenmap()]
+#'   [ggmap::get_stadiamap()]
 #'   function for details.
 #'   Defaults to `NULL` such that no basemap is shown.
 #'   Note that the \pkg{ggmap} package must be installed to show a basemap.
 #'
 #' @param maxcell `integer` Maximum number of grid cells for mapping.
 #'   Defaults to 50000.
 #'
-#' @param ... Additional arguments passed to [ggmap::get_stamenmap()].
+#' @param ... Additional arguments passed to [ggmap::get_stadiamap()].
 #'
 #' @details
 #' Note that data are automatically projected to a
@@ -110,7 +110,7 @@ NULL
 #' if (require(ggmap)) {
 #'   ## create customized map with basemap
 #'   p3 <-
-#'     plot_spp_aoh_data(spp_aoh_data, zoom = 7, maptype = "toner") +
+#'     plot_spp_aoh_data(spp_aoh_data, zoom = 7, maptype = "stamen_toner") +
 #'     scale_fill_manual(
 #'       values = c("suitable" = "blue", "not suitable" = "transparent")
 #'     ) +
@@ -310,11 +310,18 @@ plot_spp_data <- function(x, max_plot = 9, expand = 0.05,
 #'
 #' @param x [sf::st_sf()] object.
 #'
-#' @return A [ggmap::get_stamenmap()] object.
+#' @return A [ggmap::get_stadiamap()] object.
 #'
 #' @noRd
 get_ggmap_basemap <- function(x, expand = 0.05, ...) {
   assertthat::assert_that(sf::st_crs(x) == sf::st_crs(4326))
+  assertthat::assert_that(
+    nzchar(Sys.getenv("GGMAP_STADIAMAPS_API_KEY")),
+    msg = paste(
+      "StadiaMaps API key must be registered to plot a basemap,",
+      "see `?ggmap::register_stadiamaps` for details."
+    )
+  )
   bb <- as.list(sf::st_bbox(x))
   bb2 <- bb
   if (expand > 0) {
@@ -325,5 +332,5 @@ get_ggmap_basemap <- function(x, expand = 0.05, ...) {
     bb2[["ymin"]] <- bb[["ymin"]] - yf
     bb2[["ymax"]] <- bb[["ymax"]] + yf
   }
-  ggmap::get_stamenmap(unname(unlist(bb2)), ...)
+  ggmap::get_stadiamap(unname(unlist(bb2)), ...)
 }
diff --git a/R/plot_spp_frc_data.R b/R/plot_spp_frc_data.R
@@ -88,7 +88,7 @@ NULL
 #' if (require(ggmap)) {
 #'   ## create customized map with basemap
 #'   p3 <-
-#'     plot_spp_frc_data(spp_frc_data, zoom = 7, maptype = "toner") +
+#'     plot_spp_frc_data(spp_frc_data, zoom = 7, maptype = "stamen_toner") +
 #'     scale_fill_viridis_c() +
 #'     scale_color_manual(values = c("range" = "red")) +
 #'     scale_size_manual(values = c("range" = 1.5)) +

diff --git a/README.Rmd b/README.Rmd
@@ -184,7 +184,11 @@ Finally, let's create some maps to compare the range data with the Area of habit
 # create maps
 ## N.B. you might need to install the ggmap package
 map <-
-  plot_spp_aoh_data(spp_aoh_data, zoom = 6, maptype = "toner-background") +
+  plot_spp_aoh_data(
+    spp_aoh_data,
+    zoom = 6,
+    maptype = "stamen_toner_background"
+  ) +
   scale_fill_viridis_d() +
   scale_color_manual(values = c("range" = "red")) +
   scale_size_manual(values = c("range" = 0.5)) +

diff --git a/README.md b/README.md
@@ -335,7 +335,11 @@ of habitat data.
 # create maps
 ## N.B. you might need to install the ggmap package
 map <-
-  plot_spp_aoh_data(spp_aoh_data, zoom = 6, maptype = "toner-background") +
+  plot_spp_aoh_data(
+    spp_aoh_data,
+    zoom = 6,
+    maptype = "stamen_toner_background"
+  ) +
   scale_fill_viridis_d() +
   scale_color_manual(values = c("range" = "red")) +
   scale_size_manual(values = c("range" = 0.5)) +
@@ -345,7 +349,11 @@ map <-
     strip.text = element_text(color = "white"),
     strip.background = element_rect(fill = "black", color = "black")
   )
+```
+
+    ## |---------|---------|---------|---------|=========================================                                          |---------|---------|---------|---------|=========================================                                          
 
+``` r
 # display maps
 print(map)
 ```
@@ -362,7 +370,7 @@ produce Area of Habitat data.
     relevant data using:
 
       Hanson JO (2023) aoh: Create Area of Habitat Data. R package version
-      0.0.2.8. Available at https://github.com/prioritizr/aoh.
+      0.0.2.9. Available at https://github.com/prioritizr/aoh.
 
       IUCN [insert year] IUCN Red List of Threatened Species. Version
       [insert version]. Available at www.iucnredlist.org.

diff --git a/docs/404.html b/docs/404.html