Reads data Stock Synthesis file structure into a Data object using package r4ss

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

Usage

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_season = "mean",
  silent = FALSE,
  ...
)

Arguments

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, character 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_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.
silent: Logical. Suppress all messages?
...: Arguments to pass to SS_output

Value

An object of class Data.

Note

Currently supports the version of r4ss on CRAN (v.1.24) and Github (v.1.34-40). Function may be incompatible with other versions of r4ss.

Author

T. Carruthers and Q. Huynh