Run a retrospective analyses

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. To run retrospective models in parallel, use future::plan() before running retro().

Usage

retro(
  dir = getwd(),
  masterdir = lifecycle::deprecated(),
  oldsubdir = "",
  newsubdir = "retrospectives",
  subdirstart = "retro",
  years = 0:-5,
  overwrite = TRUE,
  RemoveBlocks = FALSE,
  verbose = FALSE,
  exe = "ss3",
  ...
)

Arguments

dir

Directory where everything takes place.

masterdir

Deprecated. Use dir instead.

oldsubdir

Subdirectory within dir with existing model files.

newsubdir

Subdirectory within dir 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.

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.

verbose

A logical value specifying if output should be printed to the screen.

exe

Executable name. Can be just the name of the executable file if it is in the specified directory or in the user's PATH. Can also include the absolute path or a path relative to the specified directory. Needs to be a single character string, not a vector. On Windows, exe can optionally have the .exe extension appended; on Unix-based systems (i.e., Mac and Linux), no extension should be included.

...

Additional arguments passed to run(), such as extras, show_in_console, and skipfinished.

See also

SSgetoutput()

Other run functions: copy_SS_inputs(), jitter(), populate_multiple_folders(), profile(), run(), tune_comps()

Author

Ian G. Taylor, James T. Thorson, Kathryn L. Doering, Kiva L. Oken

Examples

if (FALSE) { # \dontrun{
# note: don't run this in your main directory--make a copy in case something
# goes wrong
mydir <- "C:/Simple"

## retrospective analyses
retro(
  dir = mydir,
  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")
)

## run retrospectives in parallel
ncores <- parallelly::availableCores(omit = 1)
future::plan(future::multisession, workers = ncores)
retro(
  dir = mydir,
  years = 0:-5
)
future::plan(future::sequential)
} # }