Mercurial > repos > ecology > regionalgam_ab_index
comparison ab-index.R @ 0:d0ee713d4758 draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
| author | ecology |
|---|---|
| date | Thu, 20 Jun 2019 04:05:06 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:d0ee713d4758 |
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| 1 #!/usr/bin/env Rscript | |
| 2 | |
| 3 args = commandArgs(trailingOnly=TRUE) | |
| 4 source(args[1]) | |
| 5 | |
| 6 | |
| 7 tryCatch({input = read.table(args[2], header=TRUE,sep=" ")},finally={input = read.table(args[2], header=TRUE,sep=",")}) | |
| 8 pheno = read.table(args[3], header=TRUE,sep=" ") | |
| 9 | |
| 10 if("TREND" %in% colnames(input)){ | |
| 11 input <- input[input$TREND==1,c("SPECIES","SITE","YEAR","MONTH","DAY","COUNT")] | |
| 12 } | |
| 13 data.index <- abundance_index(input, pheno) | |
| 14 write.table(data.index, file="data.index", row.names=FALSE, sep=" ") |