Skip to contents

A function to create a list object for the output from Stock Synthesis

Source: R/SS_output.R
SS_output.Rd

Reads the Report.sso and (optionally) the covar.sso, CompReport.sso and other files produced by Stock Synthesis and formats the important content of these files into a list in the R workspace. A few statistics unavailable elsewhere are taken from the .par file. Summary information and statistics can be returned to the R console or just contained within the list produced by this function.

Usage

SS_output(
  dir = "C:/myfiles/mymodels/myrun/",
  dir.mcmc = NULL,
  repfile = "Report.sso",
  compfile = "CompReport.sso",
  covarfile = "covar.sso",
  forefile = "Forecast-report.sso",
  wtfile = "wtatage.ss_new",
  warnfile = "warning.sso",
  ncols = lifecycle::deprecated(),
  forecast = TRUE,
  warn = TRUE,
  covar = TRUE,
  readwt = TRUE,
  verbose = TRUE,
  printstats = TRUE,
  hidewarn = FALSE,
  NoCompOK = TRUE,
  aalmaxbinrange = 4,
  SpawnOutputLabel = "Spawning output"
)

Arguments

dir

A file path to the directory of interest. The default value is dir = NULL, which leads to using the current working directory.

dir.mcmc

Optional directory containing MCMC output. This can either be relative to dir, such that file.path(dir, dir.mcmc) will end up in the right place, or an absolute path.

repfile

Name of the big report file (could be renamed by user).

compfile

Name of the composition report file.

covarfile

Name of the covariance output file.

forefile

Name of the forecast file.

wtfile

Name of the file containing weight at age data.

warnfile

Name of the file containing warnings.

ncols

Deprecated. This value is now calculated automatically.

forecast

Read the forecast-report file?

warn

Read the Warning.sso file?

covar

Read covar.sso?

readwt

Read the weight-at-age file?

verbose

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

printstats

Print summary statistics about the output to the R GUI?

hidewarn

Hides some warnings output from the R GUI.

NoCompOK

Allow the function to work without a CompReport file.

aalmaxbinrange

The largest length bin range allowed for composition data to be considered as conditional age-at-length data.

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.

Value

Many values are returned. Complete list would be quite long, but should probably be created at some point in the future.

See also

SS_plots()

Author

Ian Stewart, Ian Taylor

Examples

if (FALSE) { # \dontrun{
# read model output
myreplist <- SS_output(dir = "c:/SS/Simple/")
# make a bunch of plots
SS_plots(myreplist)

# read model output and also read MCMC results (if run), which in
# this case would be stored in c:/SS/Simple/mcmc/
myreplist <- SS_output(dir = "c:/SS/Simple/", dir.mcmc = "mcmc")
} # }