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Filter higherrank results if not allowed #36

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Filter higherrank results if not allowed #36

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e4e179e
Filter higherrank results
willgearty Nov 5, 2019
8a9bb4e
Another if check
willgearty Nov 5, 2019
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18 changes: 13 additions & 5 deletions R/get_gbif_taxonomy.R
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Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,14 @@ get_gbif_taxonomy <- function(x,
}
}

#clean out higherrank matches, if not allowed
if(!higherrank) {
temp[[i]] <- subset(temp[[i]], matchtype != "HIGHERRANK")
if(nrow(temp[[i]]) == 0) {
warning_i <- paste(warning_i, "No matching species concept!")
}
}

# check for confidence threshold

if(!is.null(conf_threshold) & nrow(temp[[i]]) > 0) {
Expand Down Expand Up @@ -122,7 +130,7 @@ get_gbif_taxonomy <- function(x,

# resolve all synonyms, if allowed

if(!any(temp[[i]]$status == "ACCEPTED") & any(temp[[i]]$status == "SYNONYM")) {
if(nrow(temp[[i]]) > 0 && !any(temp[[i]]$status == "ACCEPTED") & any(temp[[i]]$status == "SYNONYM")) {
if(resolve_synonyms) {
keep <- temp[i]
temp[i] <- taxize::get_gbifid_(temp[[i]]$species[which.max(temp[[i]]$confidence)], messages = verbose)
Expand Down Expand Up @@ -158,7 +166,7 @@ get_gbif_taxonomy <- function(x,

# check for doubtful status

if(all(temp[[i]]$status == "DOUBTFUL")) {
if(nrow(temp[[i]]) > 0 && all(temp[[i]]$status == "DOUBTFUL")) {

temp[[i]] <- subset(temp[[i]], status == "DOUBTFUL")
warning_i <- paste(warning_i, "Mapped concept is labelled 'DOUBTFUL'!")
Expand All @@ -176,7 +184,7 @@ get_gbif_taxonomy <- function(x,

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

if(match(temp[[i]]$rank, rankorder) > 7 & !subspecies) {
if(nrow(temp[[i]]) > 0 && match(temp[[i]]$rank, rankorder) > 7 & !subspecies) {

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

Expand All @@ -193,7 +201,7 @@ get_gbif_taxonomy <- function(x,

}

if(temp[[i]]$matchtype == "HIGHERRANK") {
if(nrow(temp[[i]]) > 0 && temp[[i]]$matchtype == "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 All @@ -205,7 +213,7 @@ get_gbif_taxonomy <- function(x,


# 4. create structured output
if(temp[[i]]$matchtype != "NONE") {
if(nrow(temp[[i]]) > 0 && temp[[i]]$matchtype != "NONE") {

temp[[i]] <- data.frame(
scientificName = x[i],
Expand Down