SS2Data: Reads data Stock Synthesis file structure into a Data object...

In MSEtool: Management Strategy Evaluation Toolkit

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

Description

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(s)

T. Carruthers and Q. Huynh

See Also

SS2OM

MSEtool documentation built on Sept. 30, 2024, 9:22 a.m.