Usage
SS_output(dir = "C:/myfiles/mymodels/myrun/", model = "ss3",
repfile = "Report.sso", compfile = "CompReport.sso",
covarfile = "covar.sso", ncols = 200, forecast = TRUE, warn = TRUE,
covar = TRUE, checkcor = TRUE, cormax = 0.95, cormin = 0.01,
printhighcor = 10, printlowcor = 10, verbose = TRUE,
printstats = TRUE, hidewarn = FALSE, NoCompOK = FALSE,
aalmaxbinrange = 4)
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 th
forecast
Read the forecast-report file? Default=TRUE.
warn
Read the Warning.sso file? Default=TRUE.
covar
Read covar.sso to get variance information and identify
bad correlations? Default=TRUE.
checkcor
Check for bad correlations? Default=TRUE.
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=TRUE.
printstats
Print summary statistics about the output to the R
GUI? Default=TRUE.
hidewarn
Hides some warnings output from the R GUI.
Default=FALSE.
NoCompOK
Allow the function to work without a CompReport file.
Default=FALSE.
aalmaxbinrange
The largest length bin range allowed for
composition data to be considered as conditional age-at-length data.
Default=4.