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Get output from multiple Stock Synthesis models.

Source: R/SSgetoutput.R
SSgetoutput.Rd

Apply the function SS_output() multiple times and save output as individual objects or a list of lists.

Usage

SSgetoutput(
  keyvec = NULL,
  dirvec = NULL,
  getcovar = TRUE,
  getcomp = TRUE,
  forecast = TRUE,
  verbose = TRUE,
  listlists = lifecycle::deprecated(),
  underscore = FALSE,
  save.lists = FALSE,
  SpawnOutputLabel = "Spawning output",
  modelnames = NULL
)

Arguments

keyvec

A vector of strings that are appended to the output files from each model if models are all in one directory. Default=NULL.

dirvec

A vector of directories (full path or relative to working directory) in which model output is located. Default=NULL.

getcovar

Choice to read or not read covar.sso output (saves time and memory). Default=TRUE.

getcomp

Choice to read or not read CompReport.sso output (saves time and memory). Default=TRUE.

forecast

Choice to read or not read forecast quantities. Default=FALSE.

verbose

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

listlists

Deprecated argument that wasn't working.

underscore

Add an underscore '_' between any file names and any keys in keyvec. Default=FALSE.

save.lists

Save each list of parsed output as a .Rdata file (with default filenaming convention based on iteration and date stamp.

SpawnOutputLabel

An alternative to "Spawning output" for use in figure axis labels and table headers for models that include a fecundity relationship. This provides an option to provide the units, e.g. SpawnOutputLabel = "Spawning output (trillions of eggs)". This needs to be a user input because the units depend on the choice of fecundity parameters which are calculated outside of the SS3 model.

modelnames

Optional vector of model names that can be passed to downstream functions like SSsummarize(), SSplotComparisons() (where it is used in the default legend), and SStableComparisons() (where it is used in the default column names).

See also

SS_output()

Other model comparison functions: SSplotComparisons(), SSsummarize(), SStableComparisons()

Author

Ian Taylor

Examples

# contrived example where the same model is read twice
mydir <- file.path(
  path.package("r4ss"),
  file.path("extdata", "simple_small")
)
models <- SSgetoutput(
  dirvec = c(mydir, mydir),
  modelnames = c("simple_small", "simple_small_again")
)
#> ℹ length(dirvec) as input to SSgetoutput: 2
#> ℹ reading output from /home/runner/work/_temp/Library/r4ss/extdata/simple_small/Report.sso
#> ℹ added element 'simple_small' to list
#> ℹ reading output from /home/runner/work/_temp/Library/r4ss/extdata/simple_small/Report.sso
#> ℹ added element 'simple_small_again' to list