annotate gls-adjusted.R @ 0:a79f5f0f17ad draft default tip

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e

#!/usr/bin/env Rscript
library(nlme)
library(MASS)

args = commandArgs(trailingOnly=TRUE)
input1 = read.table(args[1], header=TRUE) #input1=col.index =glmmpql-output
input2 = read.table(args[2], header=TRUE,sep="	") #input2=data.index =abundance_index-output

input1<-as.matrix(input1)

year <- unique(input2$YEAR)
mod <- gls(input1~year, correlation = corARMA(p=2))
summary<-summary(mod)

save(mod, file = "mod_adjusted.rda")
capture.output(summary, file="mod_adjusted-summary.txt")