comparison glmmpql.R @ 0:b416a363a2d5 draft default tip

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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-1:000000000000 0:b416a363a2d5
1 #!/usr/bin/env Rscript
2 library(nlme)
3 library(MASS)
4
5 args = commandArgs(trailingOnly=TRUE)
6 input = read.table(args[1], header=TRUE,sep=" ")
7 glmm.mod_fullyear <- glmmPQL(regional_gam~ as.factor(YEAR)-1,data=input,family=quasipoisson,random=~1|SITE, correlation = corAR1(form = ~ YEAR | SITE),verbose = FALSE)
8
9 col.index <- as.numeric(glmm.mod_fullyear$coefficients$fixed)
10 year <- unique(input$YEAR)
11
12 write.table(col.index, file="output-glmmpql", row.names=FALSE, sep=" ")
13
14 png('output-plot.png')
15 plot(year,col.index,type='o', xlab="year",ylab="collated index")
16 invisible(dev.off())