bmaitner · Oct 19, 2026 · Oct 19, 2026 · Oct 19, 2026 · Oct 19, 2026
diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml
@@ -5,6 +5,11 @@
 # rhub::rhub_setup()
 #
 # It is unlikely that you need to modify this file manually.
+#
+# NSR modification: the "Add the drat repository" step in both jobs below, so
+# pak can install rWCVPdata (Suggests), which isn't on CRAN. pak does not read
+# DESCRIPTION's Additional_repositories. Keep that step if this file is
+# regenerated with rhub::rhub_setup().
 
 name: R-hub
 run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
@@ -56,6 +61,20 @@ jobs:
         with:
           token: ${{ secrets.RHUB_TOKEN }}
           job-config: ${{ matrix.config.job-config }}
+      - name: Add the drat repository for rWCVPdata
+        run: |
+          # rWCVPdata (Suggests) isn't on CRAN: add the repository named in
+          # DESCRIPTION's Additional_repositories to every later R session.
+          # utils is loaded first because 'repos' isn't set yet while profiles
+          # run, and utils won't set its defaults once something else has.
+          f <- Sys.getenv("R_PROFILE_USER")
+          if (!nzchar(f)) f <- path.expand("~/.Rprofile")
+          line <- paste('local({ loadNamespace("utils");',
+                        'options(repos = c(getOption("repos"),',
+                        'rWCVPdata = "https://matildabrown.github.io/drat")) })')
+          write(line, file = f, append = TRUE)
+          message("Added to ", f, ": ", line)
+        shell: Rscript {0}
       - uses: r-hub/actions/setup-deps@v1
         with:
           token: ${{ secrets.RHUB_TOKEN }}
@@ -85,6 +104,20 @@ jobs:
         with:
           token: ${{ secrets.RHUB_TOKEN }}
           job-config: ${{ matrix.config.job-config }}
+      - name: Add the drat repository for rWCVPdata
+        run: |
+          # rWCVPdata (Suggests) isn't on CRAN: add the repository named in
+          # DESCRIPTION's Additional_repositories to every later R session.
+          # utils is loaded first because 'repos' isn't set yet while profiles
+          # run, and utils won't set its defaults once something else has.
+          f <- Sys.getenv("R_PROFILE_USER")
+          if (!nzchar(f)) f <- path.expand("~/.Rprofile")
+          line <- paste('local({ loadNamespace("utils");',
+                        'options(repos = c(getOption("repos"),',
+                        'rWCVPdata = "https://matildabrown.github.io/drat")) })')
+          write(line, file = f, append = TRUE)
+          message("Added to ", f, ": ", line)
+        shell: Rscript {0}
       - uses: r-hub/actions/setup-deps@v1
         with:
           job-config: ${{ matrix.config.job-config }}

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -28,10 +28,9 @@ Suggests:
         terra,
         testthat,
         devtools,
-        BIEN,
         TNRS,
         vcr (>= 0.6.0),
         withr
 Additional_repositories: https://matildabrown.github.io/drat
-VignetteBuilder: knitr
+VignetteBuilder: knitr, rmarkdown
 RoxygenNote: 7.3.3
diff --git a/R/NSR_from_coordinates.R b/R/NSR_from_coordinates.R
@@ -18,48 +18,18 @@
 #' @import httr
 #' @keywords internal
 #' @examples \dontrun{
-#'library(BIEN)
+#'# Species and coordinates, with an id for each record
+#'occs <- data.frame(species = c("Acer rubrum", "Acer rubrum", "Acer platanoides"),
+#'                   latitude = c(45.50, 51.51, 45.50),
+#'                   longitude = c(-73.57, -0.13, -73.57),
+#'                   id = c("1", "2", "3"))
 #'
-#'# Get some data
+#'results <- NSR:::NSR_from_coordinates(occurrence_dataframe = occs)
 #'
-#'ar_occs <- BIEN_occurrence_species(species = "Acer rubrum",
-#'                                   natives.only = FALSE,
-#'                                   political.boundaries = TRUE,
-#'                                   limit=100)
+#'# Join the results back to the input
+#'merge(occs, results, by.x = "id", by.y = "input_id")
+#'}
 #'
-#'
-#'# Rename columns so that we can differentiate between coordinates declared
-#'# and coordinates inferred
-#'
-#'colnames(ar_occs)[which(colnames(ar_occs)=="country")] <- "country_declared"
-#'colnames(ar_occs)[which(colnames(ar_occs)=="state_province")] <- "state_declared"
-#'colnames(ar_occs)[which(colnames(ar_occs)=="county")] <- "county_declared"
-#'
-#'# Select needed fields and add an ID column
-#'
-#'ar_occs_subset <- ar_occs[c("scrubbed_species_binomial","latitude","longitude")]
-#'
-#'# Toss duplicates (speeds up processing)
-#'
-#'ar_occs_subset <- unique(ar_occs_subset)
-#'
-#'# Add an id column
-#'
-#'ar_occs_subset$id <- as.character(1:nrow(ar_occs_subset))
-#'
-#'# Get results
-#'
-#'results_ar <- NSR:::NSR_from_coordinates(occurrence_dataframe = ar_occs_subset)
-#'
-#'# Join results back to original data
-#'
-#'results_ar <- ar_occs_subset |>
-#'  merge(y = results_ar,by.x = c("id"),
-#'        by.y = c("input_id"))
-#'
-#'ar_occs <- ar_occs |> merge(results_ar,
-#'                            by = c("latitude","longitude","scrubbed_species_binomial"))
-#' }
 NSR_from_coordinates <- function(occurrence_dataframe,
                 ...){
 

diff --git a/man/NSR_from_coordinates.Rd b/man/NSR_from_coordinates.Rd
diff --git a/tests/testthat/setup-nsr.R b/tests/testthat/setup-nsr.R
@@ -9,10 +9,14 @@ url <- "https://nsrapi.xyz/nsr_wsb.php" # production
 # url <- "www.google.com"
 # url <- "www.hisstank.com"
 
-library("vcr") # *Required* as vcr is set up on loading
+# vcr is in Suggests: without it (as in CRAN's no-Suggests checks) the tests that replay
+# recorded API responses skip themselves
+if (requireNamespace("vcr", quietly = TRUE)) {
+  library("vcr") # *Required* as vcr is set up on loading
 
-invisible(vcr::vcr_configure(
-  dir = vcr::vcr_test_path("fixtures")
-))
+  invisible(vcr::vcr_configure(
+    dir = vcr::vcr_test_path("fixtures")
+  ))
 
-vcr::check_cassette_names()
+  vcr::check_cassette_names()
+}
diff --git a/tests/testthat/test-NSR.R b/tests/testthat/test-NSR.R
@@ -4,6 +4,8 @@ context("nsr main")
 test_that("example works", {
   # skip_if_offline(host = "r-project.org")
 
+  skip_if_not_installed("vcr")
+
   vcr::use_cassette("nsr_example", {
 
     results <- NSR(occurrence_dataframe = nsr_testfile,

diff --git a/tests/testthat/test-NSR_citations.R b/tests/testthat/test-NSR_citations.R
@@ -5,6 +5,8 @@ test_that("example works", {
   # skip_if_offline(host = "r-project.org")
 
 
+  skip_if_not_installed("vcr")
+
   vcr::use_cassette("nsr_citations", {
     citation_info <- NSR_citations(
       url = url,

diff --git a/tests/testthat/test-NSR_data_dictionary.R b/tests/testthat/test-NSR_data_dictionary.R
@@ -5,6 +5,8 @@ test_that("example works", {
   # skip_if_offline(host = "r-project.org")
 
 
+  skip_if_not_installed("vcr")
+
   vcr::use_cassette("nsr_dd", {
 
     NSR_fields <- NSR_data_dictionary(url = url,
@@ -22,6 +24,8 @@ test_that("example2 works", {
   # skip_if_offline(host = "r-project.org")
 
 
+  skip_if_not_installed("vcr")
+
   vcr::use_cassette("nsr_dd_status", {
 
     NSR_status <- NSR_data_dictionary(native_status = TRUE,

diff --git a/tests/testthat/test-NSR_political_divisions.R b/tests/testthat/test-NSR_political_divisions.R
@@ -3,6 +3,8 @@ context("nsr pol divs")
 test_that("example works", {
   # skip_if_offline(host = "r-project.org")
 
+  skip_if_not_installed("vcr")
+
   vcr::use_cassette("nsr_poldivs", {
 
     nsr_poldivs <- NSR_political_divisions(by_country = TRUE)
@@ -22,6 +24,8 @@ test_that("example works", {
 test_that("example 2 works", {
   # skip_if_offline(host = "r-project.org")
 
+  skip_if_not_installed("vcr")
+
   vcr::use_cassette("nsr_checklist", {
 
     nsr_checklists <- NSR_political_divisions(by_country = FALSE)

diff --git a/tests/testthat/test-NSR_simple.R b/tests/testthat/test-NSR_simple.R
@@ -4,6 +4,8 @@ context("nsr simple")
 test_that("example works", {
   # skip_if_offline(host = "r-project.org")
 
+  skip_if_not_installed("vcr")
+
   vcr::use_cassette("nsr_simple_example", {
 
     results <- NSR_simple(species = "Acer rubrum",
@@ -25,6 +27,8 @@ test_that("example works", {
 test_that("second example works", {
   # skip_if_offline(host = "r-project.org")
 
+  skip_if_not_installed("vcr")
+
   vcr::use_cassette("nsr_simple_example2", {
 
     results2 <- NSR_simple(species = c("Acer rubrum", "Aspen tremuloides") ,

diff --git a/tests/testthat/test-NSR_sources.R b/tests/testthat/test-NSR_sources.R
@@ -5,6 +5,8 @@ test_that("example works", {
   # skip_if_offline(host = "r-project.org")
 
 
+  skip_if_not_installed("vcr")
+
   vcr::use_cassette("nsr_sources", {
     sources <- NSR_sources(
       url = url,

diff --git a/tests/testthat/test-NSR_version.R b/tests/testthat/test-NSR_version.R
@@ -4,6 +4,8 @@ context("nsr version")
 test_that("example works", {
   # skip_if_offline(host = "r-project.org")
 
+  skip_if_not_installed("vcr")
+
   vcr::use_cassette("nsr_version", {
     NSR_version_metadata <- NSR_version(
       url = url,