comparison gls-adjusted.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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-1:000000000000 0:e2bff90af491
1 #!/usr/bin/env Rscript
2 library(nlme)
3 library(MASS)
4
5 args = commandArgs(trailingOnly=TRUE)
6 input1 = read.table(args[1], header=TRUE) #input1=col.index =glmmpql-output
7 input2 = read.table(args[2], header=TRUE,sep=" ") #input2=data.index =abundance_index-output
8
9 input1<-as.matrix(input1)
10
11 year <- unique(input2$YEAR)
12 mod <- gls(input1~year, correlation = corARMA(p=2))
13 summary<-summary(mod)
14
15 save(mod, file = "mod_adjusted.rda")
16 capture.output(summary, file="mod_adjusted-summary.txt")