SS2Data: Reads data Stock Synthesis file structure into a Data object...
In tcarruth/MSEtool: Management Strategy Evaluation Toolkit

Description Usage Arguments Value Note Author(s) See Also

A function that uses the file location of a fitted SS3 model including input files to population the various slots of an Data object.

SS2Data(
  SSdir,
  Name = "Imported by SS2Data",
  Common_Name = "",
  Species = "",
  Region = "",
  min_age_M = 1,
  gender = 1,
  comp_fleet = "all",
  comp_season = "sum",
  comp_partition = "all",
  comp_gender = "all",
  index_fleet = "SSB",
  index_season = "mean",
  ...
)

`SSdir`	A folder with Stock Synthesis input and output files in it
`Name`	The name for the Data object
`Common_Name`	Character string for the common name of the stock.
`Species`	Scientific name of the species
`Region`	Geographic region of the stock or fishery.
`min_age_M`	Currently, the Data object supports a single value of M for all ages. The argument selects the minimum age for calculating the mean of age-dependent M from the SS assessment.
`gender`	An integer index for the sex for importing biological parameters (1 = female, 2 = male).
`comp_fleet`	A vector of indices corresponding to fleets in the assessment over which to aggregate the composition (catch-at-length and catch-at-age) data. By default, characer string `"all"` will aggregate across all fleets.
`comp_season`	Integer, for seasonal models, the season for which the value of the index will be used. By default, `"mean"` will take the average across seasons.
`comp_partition`	Integer vector for selecting length/age observations that are retained (2), discarded (1), or both (0). By default, `"all"` sums over all available partitions.
`comp_gender`	Integer vector for selecting length/age observations that are female (1), male (2), or both (0), or both scaled to sum to one (3). By default, `"all"` sums over all gender codes.
`index_fleet`	Obsolete as of DLMtool version 5.4 (all indices will now be included in the AddInd slot).
`index_season`	Integer, for seasonal models, the season for which the value of the index will be used. By default, `"mean"` will take the average across seasons.
`...`	Arguments to pass to SS_output