238 genus family lookup

NAMESPACE

@@ -4,6 +4,7 @@ export(align_taxa)
 export(create_species_state_origin_matrix)
 export(create_taxonomic_update_lookup)
 export(default_version)
+export(get_apc_genus_family_lookup)
 export(load_taxonomic_resources)
 export(native_anywhere_in_australia)
 export(standardise_names)

NEWS.md

@@ -1,3 +1,11 @@
+# APCalign 1.0.2
+
+Minor update to fix 
+
+- Deal with the vignette issues that emerged on CRAN 
+- Improve "graceful failing", based on issues that have come up on github CI
+- minor formatting
+
 # APCalign 1.0.1
 
 First major release of APCalign.  A preprint is available at 

R/state_diversity_counts.R

@@ -1,8 +1,8 @@
 #' @title State- and territory-level diversity
-#' 
+#'
 #' @description
-#' For Australian states and territories, use geographic distribution data from 
-#' the APC to calculate state-level diversity for native, introduced, 
+#' For Australian states and territories, use geographic distribution data from
+#' the APC to calculate state-level diversity for native, introduced,
 #' and more complicated species origins
 #'
 #' @family diversity methods
@@ -26,6 +26,7 @@
 #'
 #' @examples
 #'  \donttest{state_diversity_counts(state = "NSW")}
+
 state_diversity_counts <- function(state,
                                    resources = load_taxonomic_resources()) {
 
@@ -77,14 +78,45 @@ state_diversity_counts <- function(state,
 
 
 #' @noRd
-get_apc_genus_family_lookup <-
-  function(resources = load_taxonomic_resources()) {
-    apc_s <- dplyr::filter(resources$APC,
-                    taxon_rank == "species")
-    dplyr::tibble(genus = word(apc_s$scientific_name, 1, 1),
-           family = apc_s$family) %>%
+create_apc_genus_family_lookup <-
+  function(resources) {
+    apc_s <- dplyr::filter(resources$APC, taxon_rank == "species")
+    dplyr::tibble(genus = word(apc_s$accepted_name_usage, 1, 1),
+                  family = apc_s$family) |>
       dplyr::distinct() -> lu
     return(lu)
   }
 
-
+#' @title Lookup Family by Genus from APC
+#'
+#' @description
+#' Retrieve the family name for a given genus using taxonomic data from the
+#' Australian Plant Census (APC).
+#'
+#' @param genus A character vector of genus names for which to retrieve the
+#'  corresponding family names.
+#' @param resources The taxonomic resources required to make the lookup. 
+#'  Loading this can be slow, so call \code{\link{load_taxonomic_resources}} 
+#'  separately to speed up this function and pass the resources in.
+#'
+#' @return A data frame with two columns: "genus", indicating the genus name, 
+#'  and "family", indicating the corresponding family name from the APC.
+#'
+#' @seealso \code{\link{load_taxonomic_resources}}
+#'
+#' @export
+#'
+#' @examples
+#'  \donttest{get_apc_genus_family_lookup(genus = c("Acacia", "Eucalyptus"))}
+get_apc_genus_family_lookup <-
+  function(genus, resources = load_taxonomic_resources()) {
+    if (is.null(resources)) {
+      message("Not finding taxonomic resources; check internet connection?")
+      return(NULL)
+    }
+    fam_lu <- create_apc_genus_family_lookup(resources = resources)
+    lu <- dplyr::tibble(genus = genus) %>%
+      dplyr::left_join(fam_lu, by = "genus")
+    if (any(is.na(lu$family))) warning("some non-matches with the APC accepted genus list, check the formatting of your genus vector.")
+    return(lu)
+  }

tests/testthat/benchmarks/family_check.csv

@@ -0,0 +1,5 @@
+genus,family
+Eucalyptus,Myrtaceae
+Pinus,Pinaceae
+Brassica,Brassicaceae
+not a species,NA

tests/testthat/test-state_diversity.R

@@ -33,3 +33,22 @@ test_that("native_anywhere_in_australia() works", {
   expect_equal(native_check, previous_check)
   expect_warning(native_anywhere_in_australia(species = "NOTASPECIES", resources = resources))
 })
+
+
+test_that("get_apc_genus_family_lookup() works", {
+  expect_warning(family_check <-
+                   get_apc_genus_family_lookup(
+                     c(
+                       "Eucalyptus",
+                       "Pinus",
+                       "Brassica",
+                       "not a species"
+                     ),
+                     resources = resources
+                   ))
+  # readr::write_csv(family_check,"tests/testthat/benchmarks/family_check.csv")
+  previous_check <- readr::read_csv("benchmarks/family_check.csv", show_col_types = FALSE)
+  expect_equal(family_check, previous_check)
+})
+
+