From f314b578b0bf32b40aa90ab7c35a310c58a6f6ef Mon Sep 17 00:00:00 2001 From: ehwenk Date: Mon, 22 Jan 2024 18:04:47 +1100 Subject: [PATCH] Update update_taxonomy.R requested changes made (before this tests passing - but didn't wait for final one) --- R/update_taxonomy.R | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/R/update_taxonomy.R b/R/update_taxonomy.R index 5ed5dba1..501e6590 100644 --- a/R/update_taxonomy.R +++ b/R/update_taxonomy.R @@ -148,7 +148,6 @@ update_taxonomy <- function(aligned_data, dplyr::bind_rows(taxa_blank) %>% dplyr::mutate( suggested_name = ifelse(is.na(suggested_name), aligned_name, suggested_name), - #suggested_name = ifelse(is.na(suggested_name), original_name, suggested_name), #should be removed update_reason = ifelse(taxonomic_status_aligned == "accepted", "aligned name accepted by APC", update_reason), taxonomic_status = ifelse(is.na(taxonomic_status), "unknown", taxonomic_status), taxonomic_dataset = ifelse(stringr::str_detect(taxonomic_dataset, "APC"), "APC", taxonomic_dataset), @@ -276,8 +275,8 @@ update_taxonomy_APC_genus <- function(data, resources) { 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, extract_genus(aligned_name), "")), - suggested_name = ifelse(taxonomic_status == "genus accepted", paste0(genus_accepted, aligned_minus_genus), NA), - suggested_name = ifelse(taxonomic_status != "genus accepted", aligned_name, suggested_name), + # if there is an APC-accepted genus, replace whatever the initial genus was with the accepted genus, otherwise the suggested name is the aligned name + suggested_name = ifelse(taxonomic_status == "genus accepted", paste0(genus_accepted, aligned_minus_genus), aligned_name), # indicate taxonomic_status of the genus name in `aligned_name` and why it needed to be updated for the `suggested_name` genus_update_reason = as.character(my_order), genus = genus_accepted,