Mercurial > repos > mnhn65mo > spocc_occ
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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| children |
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| -1:000000000000 | 0:8852afebb8f6 |
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| 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') |