SS_output {r4ss} | R Documentation |
Reads the Report.sso and (optionally) the covar.sso, CompReport.sso and other 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.
SS_output(
dir = "C:/myfiles/mymodels/myrun/",
dir.mcmc = NULL,
repfile = "Report.sso",
compfile = "CompReport.sso",
covarfile = "covar.sso",
forefile = "Forecast-report.sso",
wtfile = "wtatage.ss_new",
warnfile = "warning.sso",
ncols = NULL,
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 = TRUE,
aalmaxbinrange = 4
)
dir |
Directory containing the Stock Synthesis model output. Forward slashes or double backslashes and quotes are necessary. This can also either be an absolute path or relative to the working directory. |
dir.mcmc |
Optional directory containing MCMC output. This can either be
relative to |
repfile |
Name of the big report file (could be renamed by user). |
compfile |
Name of the composition report file. |
covarfile |
Name of the covariance output file. |
forefile |
Name of the forecast file. |
wtfile |
Name of the file containing weight at age data. |
warnfile |
Name of the file containing warnings. |
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. The default value is |
forecast |
Read the forecast-report file? |
warn |
Read the Warning.sso file? |
covar |
Read covar.sso to get variance information and identify bad correlations? |
readwt |
Read the weight-at-age file? |
checkcor |
Check for bad correlations? |
cormax |
The specified threshold for defining high correlations. A quantity with any correlation above this value is identified. |
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). |
printhighcor |
The maximum number of high correlations to print to the R GUI. |
printlowcor |
The maximum number of low correlations to print to the R GUI. |
verbose |
A logical value specifying if output should be printed to the screen. |
printstats |
Print summary statistics about the output to the R GUI? |
hidewarn |
Hides some warnings output from the R GUI. |
NoCompOK |
Allow the function to work without a CompReport file. |
aalmaxbinrange |
The largest length bin range allowed for composition data to be considered as conditional age-at-length data. |
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
## Not run:
# read model output
myreplist <- SS_output(dir = "c:/SS/Simple/")
# make a bunch of plots
SS_plots(myreplist)
# read model output and also read MCMC results (if run), which in
# this case would be stored in c:/SS/Simple/mcmc/
myreplist <- SS_output(dir = "c:/SS/Simple/", dir.mcmc = "mcmc")
## End(Not run)