r4ss (version 1.44.0)

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

Description

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 and .cor files. 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 = NULL,
  forecast = TRUE,
  warn = TRUE,
  covar = TRUE,
  readwt = TRUE,
  checkcor = TRUE,
  cormax = 0.95,
  cormin = 0.01,
  printhighcor = 10,
  printlowcor = 10,
  verbose = TRUE,
  printstats = TRUE,
  hidewarn = FALSE,
  NoCompOK = TRUE,
  aalmaxbinrange = 4
)

Arguments

dir

Directory containing the Stock Synthesis model output. Forward slashes or double backslashes and quotes are necessary. This can also either be an absolute path or relative to the 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

The maximum number of columns in files being read in. If this value is too big the function runs more slowly, too small and errors will occur. A warning will be output to the R command line if the value is too small. It should be bigger than the maximum age + 10 and the number of years + 10. The default value is NULL, which finds the optimum width.

forecast

Read the forecast-report file?

warn

Read the Warning.sso file?

covar

Read covar.sso to get variance information and identify bad correlations?

readwt

Read the weight-at-age file?

checkcor

Check for bad correlations?

cormax

The specified threshold for defining high correlations. A quantity with any correlation above this value is identified.

cormin

The specified threshold for defining low correlations. Only quantities with all correlations below this value are identified (to find variables that appear too independent from the model results).

printhighcor

The maximum number of high correlations to print to the R GUI.

printlowcor

The maximum number of low correlations to print to the R GUI.

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.

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()

Examples

# NOT RUN {
# 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")
# }
# NOT RUN {
# }