run_SS_models {r4ss}

Run multiple Stock Synthesis models

Description

Loops over a vector of directories and iteratively runs SS in each one

Usage

run_SS_models(
  dirvec = NULL,
  model = "ss",
  extras = "-nox",
  systemcmd = FALSE,
  skipfinished = TRUE,
  intern = FALSE,
  verbose = TRUE,
  exe_in_path = FALSE
)

Arguments

dirvec

List of directories containing the model files

model

Executable name or path to executable (absolute path, or relative to the working directory). First, if exe_in_path is FALSE, The function will look an executable with the same name in each element of dirvec. Then, if it is not found in each, the function will assume that model is the path to the executable and there is only 1 copy of the executable. Note that if there is an exe in your PATH with the same name, this will be used even if exe_in_path is FALSE.

extras

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

systemcmd

Should R call SS using "system" function instead of "shell". This may be required when running R in Emacs. Default = FALSE.

skipfinished

Skip any folders that already contain a Report.sso file. This can be helpful if the function is interrupted.

intern

Show output in the R console or save to a file?

verbose

Return updates of function progress to the R console?

exe_in_path

logical. If TRUE, will look for exe in the PATH. If FALSE, will look for exe in the model folders. Default = FALSE.

Value

Returns table showing which directories had model run and which had errors like missing executable or Report.sso already present

Author(s)

Ian Taylor

See Also

copy_SS_inputs(), populate_multiple_folders()

Examples

## Not run: 
extdata_mods <- system.file("extdata", package = "r4ss")
dirvec <- c(
  file.path(extdata_mods, "simple_3.30.12"),
  file.path(extdata_mods, "simple_3.30.13")
)
# if ss or ss.exe is available in both directories:
run_SS_models(dirvec = dirvec)

## End(Not run)