regionalgam_gls_adjusted: glmmpql.R annotate

annotate glmmpql.R @ 0:e2bff90af491 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 04:04:19 -0400
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0 e2bff90af491 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e ecology parents: diff changeset	1 #!/usr/bin/env Rscript
e2bff90af491 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e ecology parents: diff changeset	2 library(nlme)
e2bff90af491 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e ecology parents: diff changeset	3 library(MASS)
e2bff90af491 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e ecology parents: diff changeset	4
e2bff90af491 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e ecology parents: diff changeset	5 args = commandArgs(trailingOnly=TRUE)
e2bff90af491 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e ecology parents: diff changeset	6 input = read.table(args[1], header=TRUE,sep=" ")
e2bff90af491 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e ecology parents: diff changeset	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)
e2bff90af491 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e ecology parents: diff changeset	8
e2bff90af491 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e ecology parents: diff changeset	9 col.index <- as.numeric(glmm.mod_fullyear$coefficients$fixed)
e2bff90af491 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e ecology parents: diff changeset	10 year <- unique(input$YEAR)
e2bff90af491 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e ecology parents: diff changeset	11
e2bff90af491 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e ecology parents: diff changeset	12 write.table(col.index, file="output-glmmpql", row.names=FALSE, sep=" ")
e2bff90af491 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e ecology parents: diff changeset	13
e2bff90af491 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e ecology parents: diff changeset	14 png('output-plot.png')
e2bff90af491 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e ecology parents: diff changeset	15 plot(year,col.index,type='o', xlab="year",ylab="collated index")
e2bff90af491 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e ecology parents: diff changeset	16 invisible(dev.off())