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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 load(args[2])
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8
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9 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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10
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11 col.index <- as.numeric(glmm.mod_fullyear$coefficients$fixed)
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12 year <- unique(input$YEAR)
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13
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14 png('output-plot-trend.png')
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15 plot(year,col.index, type='o',xlab="year",ylab="collated index")
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16 abline(mod,lty=2,col="red")
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17 dev.off()
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