#!/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")
invisible(dev.off())

d<-data.frame(year,col.index)
colnames(d)<-c("year","collated index")
write.table(d,"s_trend.tsv",sep="	",row.names=FALSE)

cat("Show trend line on abundance plot")