Combine plastome_ncbi_db_names_to_exclude and ncbi_db_names_to_exclude

fernphy · Aug 3, 2024 · 35040a9 · 35040a9
1 parent 637e7df
commit 35040a9
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Showing 2 changed files with 3 additions and 7 deletions.
diff --git a/R/functions.R b/R/functions.R
@@ -6618,15 +6618,11 @@ ncbi_db_names_to_exclude <- function() {
     "Archangiopteris hokouensis Ching, 1958, non Angiopteris hokouensis Ching, 1959", #nolint
     "Polystichum imbricans subsp. curtum (Ewan) D.H.Wagner, 1979",
     "Tapeinidium denhamii (Hook.) C.Chr., 1905",
-    "Dryopteris sabae (Franch. & Sav.) C.Chr."
+    "Dryopteris sabae (Franch. & Sav.) C.Chr.",
+    "Danaea sellowiana C.Presl, 1845"
     )
 }
 
-plastome_ncbi_db_names_to_exclude <- function() {
-  # Superfluous with Danaea sellowiana C.Presl, 1845
-  "Danaea sellowiana Pr.in Corda., 1845"
-}
-
 #' Extract taxonomic names from an NCBI taxonomy database dump file
 #'
 #' Taxonomy dump files can be downloaded from the NCBI FTP server

diff --git a/_targets.R b/_targets.R
@@ -375,7 +375,7 @@ tar_plan(
   plastome_ncbi_names_raw = extract_ncbi_names(
     taxdump_zip_file,
     taxid_keep = plastome_metadata_raw,
-    names_exclude = plastome_ncbi_db_names_to_exclude(),
+    names_exclude = ncbi_db_names_to_exclude(),
     workers = 2
   ),
   # Resolve species names in plastome metadata