In eeholmes/DM: Dynamic Model

This runs a simple DM model on the A and P file from Stilliguamish.

require(DM)

## Set up the file name
  input_file <- "DemoAandP-Stilliguamish.csv"
  pkgpath <- find.package("DM")
  path=file.path(pkgpath, "doc", input_file )

## Set the input list
inputList <- list(
  firstYear=1986,
  lastYear=2011,
  MSYfirstYear=1986,
  MSYlastYear=2011,
  SRfunction="hockeyStick",
  analysisType="SS",
  includeMarineSurvival="yes",
  includeFlow="yes",
  escapementObsSD=0.25)

## Set the priors
priors <- createPriors(
  pMode=1.5, pSig=0.75, pMax=5,
  cMu=log(1000), cSig=10, cMin=log(500), cMax=log(4000),
  msMin=0,
  flowMax=0
  )

## Run DM
r1 <- runModel(path, input=inputList, priors=priors)

Output figures

plotResults(r1)

Create an html report with the figures and a summary of the model fit

writeReport(r1, input.type="Rmd", output.format="html_document")

Run multiple simulations to get multiple RERs

#run the simulations
simSamp <- 1:3000
nsims <- 10
vrap.nruns <- 10 #should be 1000
resultList <- list()
lels <- uels <- c()
for(i in 1:nsims){
  ravName <- "temp_rav.rav"
  outName <- "temp_out"
  sim <- simSamp[i]
  if(is.na(r1$tDat[sim,"Smsy"])) next
  createRAVfile(r1$bdat,r1$input,r1$tDat,r1$dat,filename=ravName, estType="sims",sim=sim, rav.options=list(lowerEscThreshold = 400))
  #the files are not needed so set save.output.as.files=FALSE
  vrapOut <- Main(InFile=ravName, OutFileBase=outName, 
                  NRuns=vrap.nruns, silent=TRUE, lcores=1,
                  save.output.as.files=FALSE)
  resultList <- c(resultList,list(vrapOut))
  tmp=ComputeRER(vrapOut)
  lels=c(lels, tmp$ERLEL)
  uels=c(uels, tmp$ERUEL)
  cat(i," ", vrapOut$time["elapsed"],"\n")
}

Histogram of RERs

hist(lels)
hist(uels)

if(file.exists("mod1.txt")) file.remove("mod1.txt")

eeholmes/DM documentation built on May 26, 2019, 3:36 p.m.