Mercurial > repos > ecology > regionalgam_gls

diff glmmpql.R @ 0:a79f5f0f17ad draft default tip

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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 04:02:41 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/glmmpql.R	Thu Jun 20 04:02:41 2019 -0400
@@ -0,0 +1,16 @@
+#!/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())