rd_output: A function to create a list object for the output from Stock...

In nathanvaughan1/DST: Decision Support Tool

Description

Reads the Report.sso and (optionally) the covar.sso, CompReport.sso and other files 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

rd_output(dir, model = "ss3", repfile = "Report.sso",
  compfile = "CompReport.sso", covarfile = "covar.sso",
  forefile = "Forecast-report.sso", wtfile = "wtatage.ss_new",
  ncols = 200, 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 = 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".
forefile	Name of the forecast file. Default="Forecast-report.sso".
wtfile	Name of the file containing weight at age data. Default="wtatage.ss_new".
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=TRUE.
warn	Read the Warning.sso file? Default=TRUE.
covar	Read covar.sso to get variance information and identify bad correlations? Default=TRUE.
readwt	Read the weight-at-age file? 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.

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 <- SS_output(dir='c:/SS/SSv3.10b/Simple/')
  
## End(Not run)

nathanvaughan1/DST documentation built on Jan. 18, 2021, 8:40 p.m.