demo/archive/caco3_analysis.R

In cboettig/warningsignals: Detection of Early Warning Signals for Catastrophic Bifurcations

# analysis.R

rm(list=ls())
##########
#require(socialR)
#script <- "caco3_analysis.R"
#gitaddr <- gitcommit(script)
#tags="warningsignals, stochpop"
#tweet_errors(script, tags=tags)
#on.exit(system("git push")) 
##########

require(warningsignals)
data(CaCO3) 
m <- fit_models(CaCO3, "LSN")

cpu <- 16
nboot <- 500
freq <- c(25, 50, 100, 200)


## Run the Analyses
sampling <- 
sampling_freq(m$const, m$timedep, cpu=cpu,
              nboot=nboot, sample_effort=freq)
save(list=ls(), file="caco3.Rdat")

taus <- 
reformat_tau_dists(
  bootstrap_tau(m$X, m$const, m$timedep, 
                cpu=cpu, nboot=nboot))
save(list=ls(), file="caco3.Rdat")

mc <- 
remove_unconverged(
  montecarlotest(m$const, m$timedep, 
                 cpu=cpu, nboot=nboot)) 
save(list=ls(), file="caco3.Rdat")

indicator_sampling <- 
indicator_sampling_freq(m, cpu, nboot,
                        sample_effort=freq) 

save(list=ls(), file="caco3.Rdat")

### Plot methods
## Original plot
#png("caco3_roc.png"); plot_roc_curves(c(list(mc), taus)); dev.off()
#upload("caco3_roc.png", script=script, gitaddr=gitaddr, tags=tags)

function(){
for(i in 1:length(freq)){
  input <- c(sampling[i], indicator_sampling[[i]])
  file <- paste("caco3_", freq[i], ".png", sep="")
  png(file); 
  plot_roc_curves(input, cex.axis=2, cex.lab=2); 
  dev.off()
  upload(file, script=script, gitaddr=gitaddr, tags=tags)

  file <- paste("dist_caco3_", freq[i], ".png", sep="")
  png(file, width=480*length(input))
  plot_dists(input, cex.axis=3, cex.lab=3.5); 
  dev.off()
  upload(file, script=script, gitaddr=gitaddr, tags=tags)
}
}