Mercurial > repos > ecology > regionalgam_autocor_acf
diff plot-trend.R @ 0:b416a363a2d5 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 04:03:31 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plot-trend.R Thu Jun 20 04:03:31 2019 -0400 @@ -0,0 +1,23 @@ +#!/usr/bin/env Rscript +library(nlme) +library(MASS) + +args = commandArgs(trailingOnly=TRUE) +input = read.table(args[1], header=TRUE,sep=" ") #input=data.index =ab_index-output +load(args[2]) + +glmm.mod_fullyear <- glmmPQL(regional_gam~ as.factor(YEAR)-1,data=input,family=quasipoisson,random=~1|SITE, correlation = corAR1(form = ~ YEAR | SITE),verbose = FALSE) + +col.index <- as.numeric(glmm.mod_fullyear$coefficients$fixed) +year <- unique(input$YEAR) + +png('output-plot-trend.png') +plot(year,col.index, type='o',xlab="year",ylab="collated index") +abline(mod,lty=2,col="red") +invisible(dev.off()) + +d<-data.frame(year,col.index) +colnames(d)<-c("year","collated index") +write.table(d,"s_trend.tsv",sep=" ",row.names=FALSE) + +cat("Show trend line on abundance plot")