SSv3_output {r4ss}R Documentation

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

Description

Reads the Report.sso and (optionally) the covar.sso 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

SSv3_output(dir = "C:/myfiles/mymodels/myrun/", model = "ss3",
repfile = "Report.sso", compfile = "CompReport.sso",
covarfile = "covar.sso", ncols = 200, forecast = T, warn = T,
covar = T, checkcor = T, cormax = 0.95, cormin = 0.01,
printhighcor = 10, printlowcor = 10, verbose = T,
printstats = T, hidewarn = F, NoCompOK = F)

Arguments

dir Locates the directory of the files to be read in, double backslashes (or forwardslashes) and quotes necessary.
model Name of the executable (leaving off the .exe). Deafult="ss3"
repfile Name of the big report file (could be renamed by user). Default="Report.sso".
compfile Name of the composition report file. Default="CompReport.sso".
covarfile Name of the covariance output file. Default="covar.sso".
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. Default=200.
forecast Read the forecast-report file? Default=T.
warn Read the Warning.sso file? Default=T.
covar Read covar.sso to get variance information and identify bad correlations? Default=T.
checkcor Check for bad correlations? Default=T.
cormax The specified threshold for defining high correlations. A quantity with any correlation above this value is identified. Default=0.95.
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). Default=0.01.
printhighcor The maximum number of high correlations to print to the R GUI. Default=10.
printlowcor The maximum number of low correlations to print to the R GUI. Default=10.
verbose Return updates of function progress to the R GUI? Default=T.
printstats Print summary statistics about the output to the R GUI? Default=T.
hidewarn Hides some warnings output from the R GUI. Default=F.
NoCompOK Allow the function to work without a CompReport file. Default=F.

Value

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

Author(s)

Ian Stewart, Ian Taylor

Examples

## Not run: 
myreplist <- SSv3_output(dir='c:/SS/SSv3.02d/Simple/')
## End(Not run)

[Package r4ss version 1.04 Index]