--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_trend.R	Fri Aug 03 08:28:22 2018 -0400
@@ -0,0 +1,17 @@
+#!/usr/bin/env Rscript
+library(nlme)
+library(MASS)
+
+args = commandArgs(trailingOnly=TRUE)
+input = read.table(args[1], header=TRUE,sep="	") #input=data.index =ab_index-output
+load(args[2])
+
+glmm.mod_fullyear <- glmmPQL(regional_gam~ as.factor(YEAR)-1,data=input,family=quasipoisson,random=~1|SITE, correlation = corAR1(form = ~ YEAR | SITE),verbose = FALSE)
+
+col.index <- as.numeric(glmm.mod_fullyear$coefficients$fixed)
+year <- unique(input$YEAR)
+
+png('output-plot-trend.png')
+plot(year,col.index, type='o',xlab="year",ylab="collated index")
+abline(mod,lty=2,col="red")
+dev.off()