Mercurial > repos > ecology > regionalgam_plot_trend
comparison plot-trend.R @ 0:58ecd15e6836 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 04:04:43 -0400 |
| parents | |
| children |
comparison
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| -1:000000000000 | 0:58ecd15e6836 |
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| 1 #!/usr/bin/env Rscript | |
| 2 library(nlme) | |
| 3 library(MASS) | |
| 4 | |
| 5 args = commandArgs(trailingOnly=TRUE) | |
| 6 input = read.table(args[1], header=TRUE,sep=" ") #input=data.index =ab_index-output | |
| 7 load(args[2]) | |
| 8 | |
| 9 glmm.mod_fullyear <- glmmPQL(regional_gam~ as.factor(YEAR)-1,data=input,family=quasipoisson,random=~1|SITE, correlation = corAR1(form = ~ YEAR | SITE),verbose = FALSE) | |
| 10 | |
| 11 col.index <- as.numeric(glmm.mod_fullyear$coefficients$fixed) | |
| 12 year <- unique(input$YEAR) | |
| 13 | |
| 14 png('output-plot-trend.png') | |
| 15 plot(year,col.index, type='o',xlab="year",ylab="collated index") | |
| 16 abline(mod,lty=2,col="red") | |
| 17 invisible(dev.off()) | |
| 18 | |
| 19 d<-data.frame(year,col.index) | |
| 20 colnames(d)<-c("year","collated index") | |
| 21 write.table(d,"s_trend.tsv",sep=" ",row.names=FALSE) | |
| 22 | |
| 23 cat("Show trend line on abundance plot") |