Merge pull request #28 from inbo/27-create-helper-build_taxonomy

Create helper `build_taxonomy()`

DESCRIPTION

@@ -22,7 +22,8 @@ BugReports: https://github.com/inbo/camtrapdp/issues
 Imports:
     cli,
     dplyr,
-    frictionless
+    frictionless,
+    purrr
 Suggests: 
     testthat (>= 3.0.0)
 Encoding: UTF-8

R/build_taxonomy.R

@@ -0,0 +1,26 @@
+#' Build a data frame with taxonomic information
+#'
+#' Builds a data frame from the `taxonomy` property in a Camera Trap Data
+#' Package object.
+#'
+#' @inheritParams version
+#' @return Data frame with the taxonomic information.
+#' @noRd
+build_taxonomy <- function(x) {
+  # Extract the taxonomic information
+  taxonomic_list <- purrr::pluck(x, "taxonomic")
+
+  # If there is no taxonomic information, return NULL
+  if (is.null(taxonomic_list)) {
+    return(NULL)
+  }
+
+  # Convert list into a data.frame
+  purrr::map(
+      taxonomic_list,
+      purrr::list_flatten,
+      name_spec = "{outer}.{inner}"
+    ) %>%
+    purrr::map(as.data.frame) %>%
+    purrr::list_rbind()
+}

tests/testthat/test-build_taxonomy.R

@@ -0,0 +1,144 @@
+test_that("build_taxonomy() returns a data frame", {
+  skip_if_offline()
+  x <- example_dataset()
+  expect_s3_class(build_taxonomy(x), "data.frame")
+})
+
+test_that("build_taxonomy() returns NULL when there is no taxonomic information", {
+  skip_if_offline()
+  x <- example_dataset()
+  x$taxonomic <- NULL
+
+  expect_null(build_taxonomy(x))
+})
+
+test_that("build_taxonomy() returns one row per species in $data$observations", {
+  skip_if_offline()
+  x <- example_dataset()
+  number_of_species <-
+    dplyr::n_distinct(x$data$observations$scientificName, na.rm = TRUE)
+
+  expect_identical(
+    nrow(build_taxonomy(x)),
+    number_of_species
+  )
+})
+
+test_that("build_taxonomy() returns the expected columns", {
+  skip_if_offline()
+  x <- example_dataset()
+  expect_named(
+    build_taxonomy(x),
+    c("scientificName", "taxonID", "taxonRank", "vernacularNames.eng",
+      "vernacularNames.nld")
+  )
+})
+
+test_that("build_taxonomy() creates a column per language for vernacularName", {
+  x <- example_dataset()
+  taxonomy_many_languages <- list(
+    list(
+      scientificName = "Anas platyrhynchos",
+      taxonID = "https://www.checklistbank.org/dataset/COL2023/taxon/DGP6",
+      taxonRank = "species",
+      vernacularNames = list(
+        eng = "mallard",
+        nld = "wilde eend",
+        est = "sinikael-part",
+        glv = "Laagh Voirrey",
+        wel = "Hwyaden Wyllt",
+        afr = "Groenkopeend"
+      )
+    )
+  )
+  x$taxonomic <- taxonomy_many_languages
+
+  # Expect 6 vernacularName columns
+  expect_length(
+    dplyr::select(build_taxonomy(x), dplyr::starts_with("vernacularNames.")),
+    6
+  )
+
+  # Expect the right vernacularName columns
+  expect_named(
+    dplyr::select(build_taxonomy(x), dplyr::starts_with("vernacularNames.")),
+    c(
+      "vernacularNames.eng", "vernacularNames.nld", "vernacularNames.est",
+      "vernacularNames.glv", "vernacularNames.wel", "vernacularNames.afr"
+    )
+  )
+})
+
+test_that("build_taxonomy() can handle missing vernacular names", {
+  x <- example_dataset()
+  # Create a taxonomy where the English vernacularName of Anas strepera is not
+  # provided.
+  taxonomy_missing_vernacular <- list(
+    list(
+      scientificName = "Anas platyrhynchos",
+      taxonID = "https://www.checklistbank.org/dataset/COL2023/taxon/DGP6",
+      taxonRank = "species",
+      vernacularNames = list(
+        eng = "mallard",
+        nld = "wilde eend"
+      )
+    ),
+    list(
+      scientificName = "Anas strepera",
+      taxonID = "https://www.checklistbank.org/dataset/COL2023/taxon/DGPL",
+      taxonRank = "species",
+      vernacularNames = list(
+        nld = "krakeend"
+      )
+    )
+  )
+  x$taxonomic <- taxonomy_missing_vernacular
+
+  # Check that we still get the `vernacularNames.` prefix
+  expect_named(
+    build_taxonomy(x),
+    c("scientificName", "taxonID", "taxonRank", "vernacularNames.eng",
+      "vernacularNames.nld")
+  )
+})
+
+test_that("build_taxonomy() fills missing values with NA when a taxonomic field
+           is only present for some of the records", {
+  x <- example_dataset()
+  taxonomy_missing_vernaculars <- list(
+    list(
+      scientificName = "Anas platyrhynchos",
+      taxonID = "https://www.checklistbank.org/dataset/COL2023/taxon/DGP6",
+      taxonRank = "species",
+      vernacularNames = list(
+        eng = "mallard"
+      )
+    ),
+    list(
+      scientificName = "Anas strepera",
+      taxonID = "https://www.checklistbank.org/dataset/COL2023/taxon/DGPL",
+      taxonRank = "species",
+      vernacularNames = list(
+        nld = "krakeend"
+      )
+    )
+  )
+  x$taxonomic <- taxonomy_missing_vernaculars
+
+  # Check that we still get the `vernacularNames.` prefix
+  expect_named(
+    build_taxonomy(x),
+    c("scientificName", "taxonID", "taxonRank", "vernacularNames.eng",
+      "vernacularNames.nld")
+  )
+  # Check that the Dutch vernacular name column contains an NA
+  expect_contains(
+    dplyr::pull(build_taxonomy(x), vernacularNames.nld),
+    NA_character_
+  )
+  # Check that the English vernacular name column contains an NA
+  expect_contains(
+    dplyr::pull(build_taxonomy(x), vernacularNames.eng),
+    NA_character_
+  )
+})