SS2DataMOM: Reads data Stock Synthesis file structure into a nested Data...

In MSEtool: Management Strategy Evaluation Toolkit

Reads data Stock Synthesis file structure into a nested Data object analogous with multiMSE

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

SS2DataMOM(SSdir, age_M = NULL, comp_partition = 2, silent = FALSE, ...)

Arguments

SSdir	A folder with Stock Synthesis input and output files in it. Alternatively,
age_M	A vector of ages to average across to calculate a single value of natural mortality. Currently, the Data object supports a single value of M for all ages. By default, NULL averages over all ages.
comp_partition	Integer vector for selecting length/age observations that are retained (2), discarded (1), or both (0). By default, only retained comps are used. If multiple codes are used, then comp matrix is the sum over all codes.
silent	Logical. Suppress messages?
...	Arguments to pass to SS_output

Value

A nested list of Data objects, with the first index by stock/sex and the second index by fleet.

Note

Currently tested on r4ss version 1.38.1-41 and SS 3.30.14.

Catches in Data@Cat are the predicted sex-specific catch calculated from the SS output.

Author(s)

Q. Huynh

See Also

SS2MOM

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