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
)
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 thatfile.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.
Value
Many values are returned. Complete list would be quite long, but should probably be created at some point in the future.
Examples
if (FALSE) {
# 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")
}