SS2Data {MSEtool}

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