Merge remote-tracking branch 'origin/master' into speed_loading

Author: dfalster

R/align_taxa.R

@@ -330,7 +330,7 @@ align_taxa <- function(original_name,
   if (!all(taxa$tocheck$checked)) {
 
   perfect_matches <- taxa$tocheck %>%
-    dplyr::filter(original_name %in% resources$`APC list (accepted)`$canonical_name) %>%
+    dplyr::filter(original_name %in% resources$APC_accepted$canonical_name) %>%
     dplyr::distinct(original_name) %>%
     nrow()
 

R/load_taxonomic_resources.R

@@ -136,6 +136,7 @@ load_taxonomic_resources <-
         accepted_name_usage_ID,
         name_type,
         taxon_rank,
+        family,
         genus
       ) %>%
       dplyr::arrange(taxonomic_status) %>%
@@ -162,21 +163,21 @@ load_taxonomic_resources <-
         trinomial = base::replace(trinomial, duplicated(trinomial), zzz),
       ) %>%
       dplyr::distinct()
-
-    taxonomic_resources[["APC list (accepted)"]] <-
+    
+    taxonomic_resources[["APC_accepted"]] <-
       APC_tmp %>%
       dplyr::filter(taxonomic_status == "accepted") %>%
       dplyr::mutate(taxonomic_dataset = "APC")
 
-    taxonomic_resources[["APC list (known names)"]] <-
+    taxonomic_resources[["APC_synonyms"]] <-
       APC_tmp %>%
       dplyr::filter(taxonomic_status != "accepted") %>%
       dplyr::mutate(taxonomic_dataset = "APC")
 
 
     if(!quiet) utils::setTxtProgressBar(pb, 2) 
     # Repeated from above - bionomial, tronomials etc
-    taxonomic_resources[["APNI names"]] <-
+    taxonomic_resources[["APNI_names"]] <-
       taxonomic_resources$APNI %>%
       dplyr::filter(name_element != "sp.") %>%
       dplyr::filter(taxon_rank %in% c("series", "subspecies", "species", "form", "variety")) %>%