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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 input = read.table(args[1], header=TRUE,sep=" ") #input=data.index =ab_index-output
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7
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8 glmm.mod_fullyear <- glmmPQL(regional_gam~ as.factor(YEAR)-1,data=input,family=quasipoisson,random=~1|SITE, correlation = corAR1(form = ~ YEAR | SITE),verbose = FALSE)
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9
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10 col.index <- as.numeric(glmm.mod_fullyear$coefficients$fixed)
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11 year <- unique(input$YEAR)
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12
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13 write.table(col.index, file="output-glmmpql", row.names=FALSE, sep=" ")
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14 #write.table(col.index, file="output-glmmpql", row.names=FALSE)
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15
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16 png('output-plot.png')
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17 plot(year,col.index,type='o', xlab="year",ylab="collated index")
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18 invisible(dev.off())
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