From cfa098cb70e8e70ab601672356b2c5de403ac311 Mon Sep 17 00:00:00 2001
From: Elizabeth Wenk <ehwenk@gmail.com>
Date: Fri, 3 Nov 2023 12:27:44 +1100
Subject: [PATCH] tweaks to functions

---
 R/build_align_taxon_names.R | 14 ++++++++++----
 R/build_update_taxon_list.R |  3 +--
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/R/build_align_taxon_names.R b/R/build_align_taxon_names.R
index 180e65b53..a2e87daa4 100644
--- a/R/build_align_taxon_names.R
+++ b/R/build_align_taxon_names.R
@@ -1,17 +1,23 @@
 build_align_taxon_names <- function(austraits, dataset) {
   
-  library(APCalign)
-  library(traits.build)
+  resources <- APCalign::load_taxonomic_resources()
   
   names_to_align <- austraits$taxonomic_updates %>%
     dplyr::filter(stringr::str_detect(dataset_id, dataset)) %>%
-    dplyr::filter(!cleaned_name %in% resources$APC$canonical_name & !cleaned_name %in% resources$APNI$canonical_name) %>%
+    dplyr::filter(!aligned_name %in% resources$APC$canonical_name & !aligned_name %in% resources$APNI$canonical_name) %>%
     dplyr::filter(is.na(taxonomic_resolution)) %>%
     dplyr::distinct(original_name)
 
   names_aligned <- 
     APCalign::align_taxa(original_name = names_to_align$original_name) %>%
-    dplyr::select(find = original_name, replace = aligned_name, reason = aligned_reason, taxonomic_resolution = taxon_rank)
+    dplyr::select(all_of(c("original_name", "aligned_name", "aligned_reason", "taxon_rank"))) %>%
+    dplyr::rename(all_of(c(
+      "find" = "original_name",
+      "replace" = "aligned_name",
+      "reason" = "aligned_reason",
+      "taxonomic_resolution" = "taxon_rank"
+    )))
   
   traits.build::metadata_add_taxonomic_changes_list(dataset, names_aligned)
+  
 }
diff --git a/R/build_update_taxon_list.R b/R/build_update_taxon_list.R
index 6fb1d9a52..418753d55 100644
--- a/R/build_update_taxon_list.R
+++ b/R/build_update_taxon_list.R
@@ -24,13 +24,12 @@ build_update_taxon_list <- function(austraits, taxon_list, replace = FALSE) {
     rename(aligned_name = canonical_name, taxon_rank_APNI = taxon_rank)
   
   # List of taxa that are explicitly excluded in metadata - don't want these in the taxon_list
-  # These should now be being excluded from `taxonomic_updates` table during processing, but good to check
+  # These should be excluded from `taxonomic_updates` table during processing, but good to check
   excluded_in_metadata <- austraits$excluded_data %>% filter(error == "Observation excluded in metadata") %>% distinct(original_name)
   
   # Start with taxonomic_updates table, which is all original names, aligned names, by dataset
   all_taxa <- 
     austraits$taxonomic_updates %>%
-    #filter(str_detect(aligned_name, "Cynochloris")) %>% ##temporary
     dplyr::select(dplyr::all_of(c("original_name", "aligned_name", "taxonomic_resolution"))) %>%
     # In case the same `original_name`, `aligned_name` combination occurs twice, but only once with `taxonomic_resolution` attached, arrange names, taxon_ranks
     dplyr::arrange(aligned_name, taxonomic_resolution) %>%