Mercurial > repos > ecology > regionalgam_gls

annotate gls.R @ 0:a79f5f0f17ad draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a79f5f0f17ad 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
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
diff changeset
2 library(nlme)
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
diff changeset
3 library(MASS)
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
diff changeset
4
a79f5f0f17ad 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)
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
diff changeset
6 input1 = read.table(args[1], header=TRUE) #input1=col.index =glmmpql-output
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
diff changeset
7 input2 = read.table(args[2], header=TRUE,sep=" ") #input2=data.index =abundance_index-output
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
diff changeset
8
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
diff changeset
9 input1<-as.matrix(input1)
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
diff changeset
10
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
diff changeset
11 year <- unique(input2$YEAR)
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
diff changeset
12 mod <- gls(input1~year)
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
diff changeset
13 summary<-summary(mod)
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
diff changeset
14
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
diff changeset
15 save(mod, file = "mod.rda")
a79f5f0f17ad planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
diff changeset
16 capture.output(summary, file="mod-summary.txt")