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

Description Usage Arguments Value Author(s) See Also Examples

View source: R/SS_output.R

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

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)

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

See Also

SS_plots

Examples

1
2
3
4
  ## Not run: 
    myreplist <- SS_output(dir='c:/SS/SSv3.10b/Simple/')
  
## End(Not run)

r4ss documentation built on May 29, 2017, 2:24 p.m.