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1 #!/usr/bin/env Rscript
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2 #library("getopt")
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3 #library(devtools)
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4 #library(RegionalGAM)
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5
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6 args = commandArgs(trailingOnly=TRUE)
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7 source(args[1])
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8
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9
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10 tryCatch({input = read.table(args[2], header=TRUE,sep=" ")},finally={input = read.table(args[2], header=TRUE,sep=",")})
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11 pheno = read.table(args[3], header=TRUE,sep=" ")
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12
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13 if("TREND" %in% colnames(input)){
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14 input <- input[input$TREND==1,c("SPECIES","SITE","YEAR","MONTH","DAY","COUNT")]
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15 }
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16 data.index <- abundance_index(input, pheno)
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17 write.table(data.index, file="data.index", row.names=FALSE, sep=" ")
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