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1 #!/usr/bin/env Rscript
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2 library(nlme)
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3 library(MASS)
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4
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5 args = commandArgs(trailingOnly=TRUE)
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6 input1 = read.table(args[1], header=TRUE) #input1=col.index =glmmpql-output
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7 input2 = read.table(args[2], header=TRUE,sep=" ") #input2=data.index =abundance_index-output
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8
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9 input1<-as.matrix(input1)
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10
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11 year <- unique(input2$YEAR)
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12 mod <- gls(input1~year, correlation = corARMA(p=2))
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13 summary<-summary(mod)
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14
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15 save(mod, file = "mod_adjusted.rda")
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16 capture.output(summary, file="mod_adjusted-summary.txt")
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