From e4e179e02637bfb7f2740306aeaf9690d58faf5a Mon Sep 17 00:00:00 2001
From: Will Gearty <willgearty@gmail.com>
Date: Tue, 5 Nov 2019 11:09:50 -0600
Subject: [PATCH 1/2] Filter higherrank results

---
 R/get_gbif_taxonomy.R | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/R/get_gbif_taxonomy.R b/R/get_gbif_taxonomy.R
index feccb5c..b24a935 100644
--- a/R/get_gbif_taxonomy.R
+++ b/R/get_gbif_taxonomy.R
@@ -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) {
@@ -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'!")
@@ -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) {
         
@@ -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.")
@@ -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], 

From 8a9bb4e09475b962081cad9b08bb4fc32482d80e Mon Sep 17 00:00:00 2001
From: Will Gearty <willgearty@gmail.com>
Date: Tue, 5 Nov 2019 12:03:43 -0600
Subject: [PATCH 2/2] Another if check

---
 R/get_gbif_taxonomy.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/get_gbif_taxonomy.R b/R/get_gbif_taxonomy.R
index b24a935..e3ffdb1 100644
--- a/R/get_gbif_taxonomy.R
+++ b/R/get_gbif_taxonomy.R
@@ -130,7 +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)