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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
author ecology
date Thu, 20 Jun 2019 04:03:31 -0400
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#!/usr/bin/env Rscript
library(nlme)
library(MASS)

args = commandArgs(trailingOnly=TRUE)
input = read.table(args[1], header=TRUE,sep="	") 
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)

write.table(col.index, file="output-glmmpql", row.names=FALSE, sep=" ")

png('output-plot.png')
plot(year,col.index,type='o', xlab="year",ylab="collated index")
invisible(dev.off())