SS_doRetro: Run retrospective analyses

In r4ss: R code for Stock Synthesis

Description

Do retrospective analyses by creating new directories, copying model files, and iteratively changing the starter file to set the number of years of data to exclude.

Usage

SS_doRetro(masterdir, oldsubdir, newsubdir='retrospectives',
subdirstart='retro', years=0:-5, overwrite=TRUE, extras="-nox",
intern=FALSE)

Arguments

masterdir	Directory where everything takes place.
oldsubdir	Subdirectory within masterdir with existing model files.
newsubdir	Subdirectory within masterdir where retrospectives will be run. Default is 'retrospectives'.
subdirstart	First part of the pattern of names for the directories in which the models will actually be run.
years	Vector of values to iteratively enter into the starter file for retrospective year. Should be zero or negative values.
overwrite	Overwrite any input files with matching names in the subdirectories where models will be run.
extras	Additional commands to use when running SS. Default = "-nox" will reduce the amound of command-line output.
intern	Display runtime information from SS in the R console (vs. saving to a file).

Author(s)

Ian Taylor

See Also

SSgetoutput

Examples

  ## Not run: 
    # note: don't run this in your main directory--make a copy in case something goes wrong
    mydir <- "C:/Simple"

    ## retrospective analyses
    SS_doRetro(masterdir=mydir, oldsubdir="", newsubdir="retrospectives", years=0:-5)
    
    retroModels <- SSgetoutput(dirvec=file.path(mydir, "retrospectives",paste("retro",0:-5,sep="")))
    retroSummary <- SSsummarize(retroModels)
    endyrvec <- retroSummary$endyrs + 0:-5
    SSplotComparisons(retroSummary, endyrvec=endyrvec, legendlabels=paste("Data",0:-5,"years"))
  
## End(Not run)

r4ss documentation built on May 2, 2019, 4:56 p.m.