Mercurial > repos > ecology > regionalgam_glmmpql
annotate glmmpql.R @ 0:f3e1b6d244a6 draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
author | ecology |
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date | Thu, 20 Jun 2019 04:03:57 -0400 |
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f3e1b6d244a6
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
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1 #!/usr/bin/env Rscript |
f3e1b6d244a6
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
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2 library(nlme) |
f3e1b6d244a6
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
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3 library(MASS) |
f3e1b6d244a6
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
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4 |
f3e1b6d244a6
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
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5 args = commandArgs(trailingOnly=TRUE) |
f3e1b6d244a6
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
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6 input = read.table(args[1], header=TRUE,sep=" ") |
f3e1b6d244a6
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
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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) |
f3e1b6d244a6
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
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8 |
f3e1b6d244a6
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
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9 col.index <- as.numeric(glmm.mod_fullyear$coefficients$fixed) |
f3e1b6d244a6
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
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10 year <- unique(input$YEAR) |
f3e1b6d244a6
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
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11 |
f3e1b6d244a6
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
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12 write.table(col.index, file="output-glmmpql", row.names=FALSE, sep=" ") |
f3e1b6d244a6
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
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13 |
f3e1b6d244a6
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
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14 png('output-plot.png') |
f3e1b6d244a6
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
parents:
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15 plot(year,col.index,type='o', xlab="year",ylab="collated index") |
f3e1b6d244a6
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam commit ffe42225fff8992501b743ebe2c78e50fddc4a4e
ecology
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16 invisible(dev.off()) |