Update develop to have new changes

R/load_taxonomic_resources.R

@@ -56,7 +56,7 @@ load_taxonomic_resources <-
       dataset_name = .data$datasetName
     ) %>%
     mutate(
-      genus = stringr::word(canonical_name, 1),
+      genus = extract_genus(canonical_name),
       taxon_rank = stringr::str_to_lower(taxon_rank),
       taxon_rank = stringr::str_replace(taxon_rank, "regnum", "kingdom"),
       taxon_rank = stringr::str_replace(taxon_rank, "classis", "class"),
@@ -82,7 +82,7 @@ load_taxonomic_resources <-
       name_element = .data$nameElement
     )  %>%
     mutate(
-      genus = stringr::word(canonical_name, 1),
+      genus = extract_genus(canonical_name),
       taxon_rank = stringr::str_to_lower(taxon_rank),
       taxon_rank = stringr::str_replace(taxon_rank, "regnum", "kingdom"),
       taxon_rank = stringr::str_replace(taxon_rank, "classis", "class"),
@@ -121,7 +121,7 @@ load_taxonomic_resources <-
         ),
         binomial = ifelse(is.na(binomial), zzz, binomial),
         binomial = base::replace(binomial, duplicated(binomial), zzz),
-        genus = stringr::word(stripped_canonical, 1),
+        genus = extract_genus(stripped_canonical),
         trinomial = stringr::word(stripped_canonical2, start = 1, end = 3),
         trinomial = ifelse(is.na(trinomial), zzz, trinomial),
         trinomial = base::replace(trinomial, duplicated(trinomial), zzz),
@@ -159,7 +159,7 @@ load_taxonomic_resources <-
         trinomial = stringr::word(stripped_canonical2, start = 1, end = 3),
         trinomial = ifelse(is.na(trinomial), "zzzz zzzz", trinomial),
         trinomial = base::replace(trinomial, duplicated(trinomial), "zzzz zzzz"),
-        genus = stringr::word(stripped_canonical, 1),
+        genus = extract_genus(stripped_canonical),
         taxonomic_dataset = "APNI"
       ) %>%
       dplyr::distinct() %>%

R/match_taxa.R

@@ -84,7 +84,7 @@ match_taxa <- function(
         update_na_with(strip_names_2(cleaned_name)),
       trinomial = stringr::word(stripped_name2, start = 1, end = 3),
       binomial = stringr::word(stripped_name2, start = 1, end = 2),
-      genus = stringr::word(original_name, start = 1, end = 1),
+      genus = extract_genus(original_name),
       fuzzy_match_genus =
         fuzzy_match_genera(genus, resources$genera_accepted$canonical_name),
       fuzzy_match_genus_known =

R/standardise_names.R

@@ -98,3 +98,27 @@ standardise_names <- function(taxon_names) {
     stringr::str_squish()
 }
 
+#' Extract Genus
+#' 
+#' This function extracts the genus component of a scientific name. 
+#' It identifies if the genus is/is not a hybrid. For a hybrid genus,
+#' the first two words of the taxon name are extracted (e.g. "x Cynochloris"),
+#' while for a non-hybrid genus just the first word is extracted (e.g. "Banksia").
+#'
+#' @param taxon_name 
+#'
+#' @return The genus for a scientific name.
+#'
+#' @examples
+#' genus = extract_genus(stripped_name)
+#' 
+#' 
+extract_genus <- function(taxon_name) {
+  genus <- 
+    ifelse(
+      stringr::word(taxon_name, 1) == "x",
+      stringr::word(taxon_name, start = 1, end = 2),
+      stringr::word(taxon_name, 1)
+    )
+  genus
+}

R/update_taxonomy.R

@@ -97,7 +97,7 @@ update_taxonomy <- function(aligned_data,
     aligned_data %>%
     dplyr::select(original_name, aligned_name, taxon_rank, taxonomic_dataset, aligned_reason) %>%
     dplyr::mutate(
-      genus = stringr::word(aligned_name, 1),
+      genus = extract_genus(aligned_name),
       row_number = dplyr::row_number()
     )
 
@@ -267,7 +267,7 @@ relevel_taxonomic_status_preferred_order <- function(taxonomic_status) {
 # Function to update names of taxa whose aligned_names are 
 # taxon_rank = genus and taxonomic_dataset = APC
 update_taxonomy_APC_genus <- function(data, resources) {
-  
+
   if(is.null(data)) return(NULL)
 
   data %>% 
@@ -300,7 +300,7 @@ update_taxonomy_APC_genus <- function(data, resources) {
       taxonomic_status = ifelse(is.na(accepted_name_usage_ID), as.character(my_order), paste("genus", taxonomic_status_genus)),
       taxon_ID_genus = resources$genera_all$taxon_ID[match(accepted_name_usage_ID, resources$genera_all$accepted_name_usage_ID)],
       # genus names in `aligned_name` that are not APC-accepted need to be updated to their current name in `suggested_name`
-      aligned_minus_genus = ifelse(is.na(genus_accepted), NA, stringr::str_replace(aligned_name, stringr::word(aligned_name, 1), "")),
+      aligned_minus_genus = ifelse(is.na(genus_accepted), NA, stringr::str_replace(aligned_name, extract_genus(aligned_name), "")),
       suggested_name = ifelse(taxonomic_status == "accepted", paste0(genus_accepted, aligned_minus_genus), NA),
       suggested_name = ifelse(taxonomic_status != "accepted", aligned_name, suggested_name),
       # indicate taxonomic_status of the genus name in `aligned_name` and why it needed to be updated for the `suggested_name`
@@ -341,10 +341,10 @@ update_taxonomy_APNI_genus <- function(data, resources) {
     ) %>%
     # the `suggested_name` is set to the aligned_name and other columns are set to NA
     dplyr::mutate(
-      genus = NA_character_, # genera only in APNI don't appear in this column
       accepted_name = NA_character_,
       suggested_name = aligned_name,
-      taxonomic_status_genus = "unplaced"
+      taxonomic_status_genus = "genus unplaced by APC",
+      taxonomic_status = "genus unplaced by APC",
     )
 }
 
@@ -379,8 +379,7 @@ update_taxonomy_APC_species_and_infraspecific_taxa <- function(data, resources,
     dplyr::filter(species_and_infraspecific(taxon_rank)) %>%
     dplyr::distinct(canonical_name, .keep_all = TRUE) %>%
     dplyr::select(canonical_name, accepted_name_usage_ID)
-
-
+
   split_taxa_table <- 
     resources$APC %>%
     dplyr::filter(species_and_infraspecific(taxon_rank)) %>%
@@ -495,8 +494,7 @@ update_taxonomy_APC_species_and_infraspecific_taxa <- function(data, resources,
         dplyr::select(
           aligned_name,
           taxonomic_status_aligned,
-          accepted_name_usage_ID,
-          scientific_name_ID
+          accepted_name_usage_ID
         )
     ) %>%
     ## Second, find accepted names for each name in the species (and infraspecific taxon) list (sometimes they are the same)
@@ -515,6 +513,7 @@ update_taxonomy_APC_species_and_infraspecific_taxa <- function(data, resources,
           accepted_name,
           taxonomic_status,
           scientific_name,
+          scientific_name_ID,
           family,
           subclass,
           taxon_distribution
@@ -548,7 +547,7 @@ update_taxonomy_APC_species_and_infraspecific_taxa <- function(data, resources,
       suggested_name = ifelse(is.na(suggested_name), aligned_name, suggested_name),
       taxonomic_status = ifelse(is.na(accepted_name),  taxonomic_status_aligned, "accepted"),
       # for APC-accepted species, the `genus` is the first word of the `accepted_name`
-      genus_accepted = stringr::word(suggested_name, 1),
+      genus_accepted = extract_genus(suggested_name),
       taxon_ID_genus = resources$genera_all$taxon_ID[match(genus_accepted, resources$genera_all$canonical_name)],
       update_reason =  taxonomic_status_aligned,
       taxonomic_dataset = "APC",
@@ -629,7 +628,10 @@ update_taxonomy_APNI_species_and_infraspecific_taxa <- function(data, resources)
     ## have proper columns filled in (`genus` & `taxonomic_ID_genus` & `taxonomic_dataset_genus`),
     ## while APNI names that do not align with an APC-accepted genus have these columns set to NA
     dplyr::mutate(
-      genus = ifelse(is.na(accepted_name_usage_ID_genus), NA_character_, resources$genera_all$canonical_name[match(accepted_name_usage_ID_genus, resources$genera_all$taxon_ID)]),
+      genus = ifelse(
+        is.na(accepted_name_usage_ID_genus), 
+        genus, 
+        resources$genera_all$canonical_name[match(accepted_name_usage_ID_genus, resources$genera_all$taxon_ID)]),
       taxon_ID_genus = resources$genera_all$taxon_ID[match(genus, resources$genera_all$canonical_name)],
       taxonomic_dataset_genus = ifelse(stringr::str_detect(taxonomic_dataset_genus, "APC"), "APC", taxonomic_dataset_genus)
     ) %>%

tests/testthat/benchmarks/consistency_lookup.csv

@@ -7,7 +7,7 @@ Acacia paraneura,Acacia paraneura,Exact match of taxon name to an APC-accepted c
 Athrotaxis laxiflolia,Arthrotaxis laxifolia,Fuzzy match of taxon name to an APC-known canonical name once punctuation and filler words are removed (2023-08-17),APC,https://id.biodiversity.org.au/instance/apni/951456,orthographic variant,NA,https://id.biodiversity.org.au/node/apni/7555184,Athrotaxis x laxifolia,Hook.,https://id.biodiversity.org.au/name/apni/245642,species,accepted,Cupressaceae,Pinidae,Tas,https://id.biodiversity.org.au/node/apni/7555184,Athrotaxis
 Banksia integrifolia,Banksia integrifolia,Exact match of taxon name to an APC-accepted canonical name once punctuation and filler words are removed (2023-08-17),APC,https://id.biodiversity.org.au/node/apni/2892579,accepted,misapplied,https://id.biodiversity.org.au/node/apni/2892579,Banksia integrifolia,L.f.,https://id.biodiversity.org.au/name/apni/107602,species,accepted,Proteaceae,Magnoliidae,"WA (naturalised), Qld, NSW, NI (naturalised), Vic, Tas",https://id.biodiversity.org.au/node/apni/2892579,Banksia
 Commersonia rosea,Commersonia rosea,Exact match of taxon name to an APC-known canonical name once punctuation and filler words are removed (2023-08-17),APC,https://id.biodiversity.org.au/instance/apni/924361,basionym,NA,https://id.biodiversity.org.au/node/apni/2902836,Androcalva rosea,(S.A.J.Bell & L.M.Copel.) C.F.Wilkins & Whitlock,https://id.biodiversity.org.au/name/apni/188176,species,accepted,Malvaceae,Magnoliidae,NSW,https://id.biodiversity.org.au/node/apni/2902836,Androcalva
-Galactia striata,Galactia sp. [Galactia striata],Exact match of the first word of the taxon name to an APC-accepted genus (2023-08-17),APNI,NA,unplaced by APC,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+Galactia striata,Galactia sp. [Galactia striata],Exact match of the first word of the taxon name to an APC-accepted genus (2023-08-17),APNI,NA,unplaced by APC,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Galactia
 Genoplesium insigne,Genoplesium insigne,Exact match of taxon name to an APC-known canonical name once punctuation and filler words are removed (2023-08-17),APC,https://id.biodiversity.org.au/instance/apni/51441225,nomenclatural synonym,NA,https://id.biodiversity.org.au/taxon/apni/51441228,Corunastylis insignis,(D.L.Jones) D.L.Jones & M.A.Clem.,https://id.biodiversity.org.au/name/apni/167942,species,accepted,Orchidaceae,Magnoliidae,NSW,https://id.biodiversity.org.au/taxon/apni/51441228,Corunastylis
 Hibbertia sericea,Hibbertia sericea,Exact match of taxon name to an APC-accepted canonical name once punctuation and filler words are removed (2023-08-17),APC,https://id.biodiversity.org.au/instance/apni/912933,pro parte misapplied,misapplied | pro parte misapplied,https://id.biodiversity.org.au/node/apni/2899370,Hibbertia crinita,Toelken,https://id.biodiversity.org.au/name/apni/90852,species,accepted,Dilleniaceae,Magnoliidae,"SA, Vic",https://id.biodiversity.org.au/node/apni/2899370,Hibbertia
 Hibbertia sericea,Hibbertia sericea,Exact match of taxon name to an APC-accepted canonical name once punctuation and filler words are removed (2023-08-17),APC,https://id.biodiversity.org.au/instance/apni/912932,pro parte misapplied,misapplied | pro parte misapplied,https://id.biodiversity.org.au/node/apni/2899370,Hibbertia crinita,Toelken,https://id.biodiversity.org.au/name/apni/90852,species,accepted,Dilleniaceae,Magnoliidae,"SA, Vic",https://id.biodiversity.org.au/node/apni/2899370,Hibbertia
@@ -43,7 +43,7 @@ Hibbertia sericea,Hibbertia sericea,Exact match of taxon name to an APC-accepted
 Hibbertia sericea,Hibbertia sericea,Exact match of taxon name to an APC-accepted canonical name once punctuation and filler words are removed (2023-08-17),APC,https://id.biodiversity.org.au/instance/apni/916524,pro parte misapplied,misapplied | pro parte misapplied,https://id.biodiversity.org.au/node/apni/2901708,Hibbertia simulans,Toelken,https://id.biodiversity.org.au/name/apni/90852,species,accepted,Dilleniaceae,Magnoliidae,NSW,https://id.biodiversity.org.au/node/apni/2901708,Hibbertia
 Hibbertia sericea,Hibbertia sericea,Exact match of taxon name to an APC-accepted canonical name once punctuation and filler words are removed (2023-08-17),APC,https://id.biodiversity.org.au/instance/apni/916556,pro parte misapplied,misapplied | pro parte misapplied,https://id.biodiversity.org.au/node/apni/2910589,Hibbertia superans,Toelken,https://id.biodiversity.org.au/name/apni/90852,species,accepted,Dilleniaceae,Magnoliidae,NSW,https://id.biodiversity.org.au/node/apni/2910589,Hibbertia
 Hibbertia sericea,Hibbertia sericea,Exact match of taxon name to an APC-accepted canonical name once punctuation and filler words are removed (2023-08-17),APC,https://id.biodiversity.org.au/instance/apni/916566,pro parte misapplied,misapplied | pro parte misapplied,https://id.biodiversity.org.au/node/apni/2915755,Hibbertia villifera,Tepper ex Toelken,https://id.biodiversity.org.au/name/apni/90852,species,accepted,Dilleniaceae,Magnoliidae,SA,https://id.biodiversity.org.au/node/apni/2915755,Hibbertia
-Hibbertia sp.,Hibbertia sp.,Exact match of taxon name ending with `sp.` to an APC accepted genus (2023-08-17),APNI,NA,unplaced by APC,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+Hibbertia sp.,Hibbertia sp.,Exact match of taxon name ending with `sp.` to an APC accepted genus (2023-08-17),APNI,NA,unplaced by APC,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Hibbertia
 Hibbertia stricta,Hibbertia stricta,Exact match of taxon name to an APC-accepted canonical name once punctuation and filler words are removed (2023-08-17),APC,https://id.biodiversity.org.au/instance/apni/910062,pro parte misapplied,taxonomic synonym | misapplied | pro parte misapplied,https://id.biodiversity.org.au/node/apni/2906127,Hibbertia australis,N.A.Wakef.,https://id.biodiversity.org.au/name/apni/91036,species,accepted,Dilleniaceae,Magnoliidae,"SA, Vic",https://id.biodiversity.org.au/node/apni/2906127,Hibbertia
 Hibbertia stricta,Hibbertia stricta,Exact match of taxon name to an APC-accepted canonical name once punctuation and filler words are removed (2023-08-17),APC,https://id.biodiversity.org.au/instance/apni/916725,pro parte misapplied,taxonomic synonym | misapplied | pro parte misapplied,https://id.biodiversity.org.au/node/apni/2915804,Hibbertia devitata,Toelken,https://id.biodiversity.org.au/name/apni/91036,species,accepted,Dilleniaceae,Magnoliidae,"SA, Vic",https://id.biodiversity.org.au/node/apni/2915804,Hibbertia
 Hibbertia stricta,Hibbertia stricta,Exact match of taxon name to an APC-accepted canonical name once punctuation and filler words are removed (2023-08-17),APC,https://id.biodiversity.org.au/instance/apni/916770,pro parte misapplied,taxonomic synonym | misapplied | pro parte misapplied,https://id.biodiversity.org.au/taxon/apni/51300211,Hibbertia glebosa,Toelken,https://id.biodiversity.org.au/name/apni/91036,species,accepted,Dilleniaceae,Magnoliidae,SA,https://id.biodiversity.org.au/taxon/apni/51300211,Hibbertia

tests/testthat/test-alignment_executes.R

@@ -191,7 +191,7 @@ test_that("handles APNI taxa and genus level IDs",{
   original_name <- c("Acacia sp.", "Dendropanax amplifolius", "Acanthopanax divaricatum", "Eucalyptus sp.")
   taxon_rank <- c("genus", "species", "species", "genus")
   taxonomic_dataset <- c("APC", "APNI", "APNI", "APC")
-  genus_updated <- c("Acacia", NA, NA, "Eucalyptus")
+  genus_updated <- c("Acacia", "Dendropanax", "Acanthopanax", "Eucalyptus")
 
   out1 <- 
     align_taxa(original_name, resources = resources)