Mercurial > repos > mnhn65mo > regionalgam
comparison ab_index.R @ 0:5b126f770671 draft
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| author | mnhn65mo |
|---|---|
| date | Fri, 03 Aug 2018 08:28:22 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:5b126f770671 |
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| 1 #!/usr/bin/env Rscript | |
| 2 #library("getopt") | |
| 3 #library(devtools) | |
| 4 #library(RegionalGAM) | |
| 5 | |
| 6 args = commandArgs(trailingOnly=TRUE) | |
| 7 source(args[1]) | |
| 8 | |
| 9 | |
| 10 tryCatch({input = read.table(args[2], header=TRUE,sep=" ")},finally={input = read.table(args[2], header=TRUE,sep=",")}) | |
| 11 pheno = read.table(args[3], header=TRUE,sep=" ") | |
| 12 | |
| 13 if("TREND" %in% colnames(input)){ | |
| 14 input <- input[input$TREND==1,c("SPECIES","SITE","YEAR","MONTH","DAY","COUNT")] | |
| 15 } | |
| 16 data.index <- abundance_index(input, pheno) | |
| 17 write.table(data.index, file="data.index", row.names=FALSE, sep=" ") |