comparison spocc_occ.R @ 0:8852afebb8f6 draft

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author mnhn65mo
date Thu, 02 Aug 2018 04:33:51 -0400
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-1:000000000000 0:8852afebb8f6
1 #!/usr/bin/Rscript
2
3 library(spocc)
4
5
6 ##Def functions :
7 help<-function(){
8 cat("HELP\n")
9 cat("Spocc::occ, Search on a single species name, or many. And search across a single or many data sources.\n\n")
10 cat("Need 3 args :\n")
11 cat(" - query : (character) One to many scientific names.\n")
12 cat(" - from : (character) Data source to get data from, any combination of gbif, bison, inat,ebird, ecoengine and/or vertnet.\n")
13 cat(" - limit : (numeric) Number of records to return. This is passed across all sources.\n")
14 q("no")
15 }
16
17 formatSpName <- function(spName) paste(strsplit(spName, split=' ')[[1]], collapse='_') ###Wallace function
18
19 ####################################
20
21 args = commandArgs(trailingOnly=TRUE)
22
23 #Help display
24 if(args[1]=="-h" || args[1]=="--help" || length(args)<3){help()}
25
26 #Get args
27 sname<-args[1]
28 dbase_input<-args[2]
29 max<-as.integer(args[3])
30
31 #Get all databases
32 bases<-strsplit(dbase_input,",")
33 dbase<-c()
34 for (base in bases){
35 dbase<-c(dbase,base)
36 }
37
38 #Get occurrences
39 results <- spocc::occ(query=sname, from=dbase, limit=max, has_coords=TRUE)
40
41 #Dispay results
42 if(length(dbase)==1){
43 results_data <- results[[dbase[1]]]$data[[formatSpName(sname)]]
44 }else{
45 res <- occ2df(results)
46 results_data <- res
47 }
48
49 results_data<-as.matrix(results_data)
50
51 #If empty
52 if(length(results_data)==0){cat("\nNo occurrences found.\nLittle tip : Check your input typo, some databases are case sensitive : Genus species.\n")}
53
54 #Write them
55 write.table(file="output.tab",results_data,sep="\t",row.names=FALSE)
56
57 q('no')