Mercurial > repos > ecology > regionalgam_plot_trend
diff ab-index.R @ 0:58ecd15e6836 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 04:04:43 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ab-index.R Thu Jun 20 04:04:43 2019 -0400 @@ -0,0 +1,14 @@ +#!/usr/bin/env Rscript + +args = commandArgs(trailingOnly=TRUE) +source(args[1]) + + +tryCatch({input = read.table(args[2], header=TRUE,sep=" ")},finally={input = read.table(args[2], header=TRUE,sep=",")}) +pheno = read.table(args[3], header=TRUE,sep=" ") + +if("TREND" %in% colnames(input)){ + input <- input[input$TREND==1,c("SPECIES","SITE","YEAR","MONTH","DAY","COUNT")] +} +data.index <- abundance_index(input, pheno) +write.table(data.index, file="data.index", row.names=FALSE, sep=" ")