r4ss (version 1.44.0)

SS_doRetro: Run retrospective analyses

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. Note that there was a bug for retrospectives in 3.30.01; the user should update their model to a newer version of Stock Synthesis to run retrospectives

Usage

SS_doRetro(
  masterdir,
  oldsubdir,
  newsubdir = "retrospectives",
  subdirstart = "retro",
  years = 0:-5,
  overwrite = TRUE,
  exefile = "ss",
  extras = "-nox",
  intern = FALSE,
  CallType = "system",
  RemoveBlocks = 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.

exefile

Executable file found in directory with model files. On Windows systems, this value will be automatically updated if a single executable exists in the directory of model files. Input exefile=NULL if the executable is in your path and doesn't need copying.

extras

Additional commands to use when running SS. Default = "-nox" will reduce the amount of command-line output.

intern

Display runtime information from SS in the R console (vs. saving to a file).

CallType

Either "system" or "shell" (choice depends on how you're running R. Default is "system".

RemoveBlocks

Logical switch determining whether specifications of blocks is removed from top of control file. Blocks can cause problems for retrospective analyses, but the method for removing them is overly simplistic and probably won't work in most cases. Default=FALSE.

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")
)
# }
# NOT RUN {
# }