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get_gbif_taxonomy.R - issue #48 #49

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1dd22fd
Update get_gbif_taxonomy.R
Ivypillar Jan 20, 2026
e66b256
Update get_gbif_taxonomy.R
Ivypillar Jan 20, 2026
657586a
Update get_gbif_taxonomy.R
Ivypillar Jan 20, 2026
b61e388
Update get_gbif_taxonomy.R
Ivypillar Jan 20, 2026
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14 changes: 8 additions & 6 deletions R/get_gbif_taxonomy.R
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Original file line number Diff line number Diff line change
Expand Up @@ -140,8 +140,10 @@ get_gbif_taxonomy <- function(x,

# resolve all synonyms, if allowed

if(!any(temp[[i]]$status == "ACCEPTED") & any(temp[[i]]$status == "SYNONYM")) {
if(!any(temp[[i]]$status == "ACCEPTED") & any(temp[[i]]$status == "SYNONYM") & any(temp[[i]]$rank == "species")) {
if(resolve_synonyms) {


keep <- temp[i]
temp[i] <- taxize::get_gbifid_(temp[[i]]$species[which.max(temp[[i]]$confidence)], messages = verbose)
if(temp[[i]][1,]$status == "ACCEPTED") {
Expand Down Expand Up @@ -193,8 +195,10 @@ get_gbif_taxonomy <- function(x,
# 3. check rankorder of result

rankorder <- c("kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies")

if(match(temp[[i]]$rank, rankorder) > 7 & !subspecies) {
#print(temp)
#print(temp[[i]]$rank[1])
#print(rankorder)
if(match(temp[[i]]$rank[1], rankorder) > 7 & !subspecies) {

if(length(strsplit(as.character(temp[[i]]$canonicalname), " ")[[1]]) > 2) {

Expand All @@ -211,7 +215,7 @@ get_gbif_taxonomy <- function(x,

}

if(temp[[i]]$matchtype == "HIGHERRANK") {
if(temp[[i]]$matchtype[1] == "HIGHERRANK") {
if(higherrank) {
temp[[i]] <- subset(temp[[i]], temp[[i]]$confidence == max(temp[[i]]$confidence))
warning_i <- paste(warning_i, "No matching species concept! Entry has been mapped to higher taxonomic level.")
Expand Down Expand Up @@ -257,8 +261,6 @@ get_gbif_taxonomy <- function(x,

return(out)



}


Expand Down