diff spocc_occ.R @ 0:8852afebb8f6 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spocc_occ.R	Thu Aug 02 04:33:51 2018 -0400
@@ -0,0 +1,57 @@
+#!/usr/bin/Rscript
+
+library(spocc)
+
+
+##Def functions :
+help<-function(){
+    cat("HELP\n")
+    cat("Spocc::occ, Search on a single species name, or many. And search across a single or many data sources.\n\n")
+    cat("Need 3 args :\n")
+    cat("    - query : (character) One to many scientific names.\n")
+    cat("    - from : (character)  Data source to get data from, any combination of gbif, bison, inat,ebird, ecoengine and/or vertnet.\n")
+    cat("    - limit : (numeric) Number of records to return. This is passed across all sources.\n")
+    q("no")
+}
+
+formatSpName <- function(spName) paste(strsplit(spName, split=' ')[[1]], collapse='_') ###Wallace function
+
+####################################
+
+args = commandArgs(trailingOnly=TRUE)
+
+#Help display
+if(args[1]=="-h" || args[1]=="--help" || length(args)<3){help()}
+
+#Get args
+sname<-args[1]
+dbase_input<-args[2]
+max<-as.integer(args[3])
+
+#Get all databases
+bases<-strsplit(dbase_input,",")
+dbase<-c()
+for (base in bases){
+    dbase<-c(dbase,base)
+}
+
+#Get occurrences
+results <- spocc::occ(query=sname, from=dbase, limit=max, has_coords=TRUE)
+
+#Dispay results
+if(length(dbase)==1){
+    results_data <- results[[dbase[1]]]$data[[formatSpName(sname)]]
+}else{
+    res <- occ2df(results)
+    results_data <- res
+}
+
+results_data<-as.matrix(results_data)
+
+#If empty
+if(length(results_data)==0){cat("\nNo occurrences found.\nLittle tip : Check your input typo, some databases are case sensitive : Genus species.\n")}
+
+#Write them
+write.table(file="output.tab",results_data,sep="\t",row.names=FALSE)
+
+q('no')