Description Usage Arguments Value Author(s) See Also Examples
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.
1 2 3 4 5 6 7 8 | SS_output(dir = "C:/myfiles/mymodels/myrun/", 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)
|
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. |
Many values are returned. Complete list would be quite long, but should probably be created at some point in the future.
Ian Stewart, Ian Taylor
1 2 3 4 | |
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