Summarize the output from multiple Stock Synthesis models.

Summarize various quantities from the model output collected by SSgetoutput() and return them in a list of tables and vectors. If the models have incompatible dimensions, some quantities can't be compared via this function, such as selectivity.

Usage

SSsummarize(
  biglist,
  sizeselfactor = "Lsel",
  ageselfactor = "Asel",
  selfleet = NULL,
  selyr = "startyr",
  selgender = lifecycle::deprecated(),
  selsex = 1,
  SpawnOutputUnits = NULL,
  lowerCI = 0.025,
  upperCI = 0.975,
  verbose = TRUE
)

Arguments

biglist

A list of lists, one for each model. The individual lists can be created by SS_output() or the list of lists can be created by SSgetoutput() (which iteratively calls SS_output()).

sizeselfactor

A string or vector of strings indicating which elements of the selectivity at length output to summarize. Default=c("Lsel").

ageselfactor

A string or vector of strings indicating which elements of the selectivity at age output to summarize. Default=c("Asel").

selfleet

Vector of fleets for which selectivity will be summarized. NULL=all fleets. Default=NULL.

selyr

String or vector of years for which selectivity will be summarized. NOTE: NOT CURRENTLY WORKING. Options: NULL=all years, "startyr" = first year.

selgender

Deprecated. Use selsex instead.

selsex

Vector of sexes (1 and/or 2) for which selectivity will be summarized. NULL=all sexes. Default=NULL.

SpawnOutputUnits

Optional single value or vector of "biomass" or "numbers" giving units of spawning for each model.

lowerCI

Quantile for lower bound on calculated intervals. Default = 0.025 for 95% intervals.

upperCI

Quantile for upper bound on calculated intervals. Default = 0.975 for 95% intervals.

verbose

A logical value specifying if output should be printed to the screen.

See also

SSgetoutput()

Author

Ian Taylor