SS2OM: Reads MLE estimates from Stock Synthesis file structure into...

Description Usage Arguments Details Value Note Author(s) See Also

View source: R/SS2OM.R

Description

A function that uses the file location of a fitted SS3 model including input files to population the various slots of an operating model with MLE parameter estimates. The function mainly populates the Stock and Fleet portions of the operating model; the user still needs to parameterize most of the observation and implementation portions of the operating model.

Usage

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SS2OM(SSdir, nsim = 48, proyears = 50, reps = 1, maxF = 3, seed = 1,
  Obs = DLMtool::Generic_Obs, Imp = DLMtool::Perfect_Imp, Name = NULL,
  Source = "No source provided", Author = "No author provided", ...)

Arguments

SSdir

A folder with Stock Synthesis input and output files in it

nsim

The number of simulations to take for parameters with uncertainty (for [email protected] custom parameters).

proyears

The number of projection years for MSE

reps

The number of stochastic replicates within each simulation in the operating model.

maxF

The maximum allowable F in the operating model.

seed

The random seed for the operating model.

Obs

The observation model (class Obs).

Imp

The implementation model (class Imp).

Name

The name of the operating model

Source

Reference to assessment documentation e.g. a url

Author

Who did the assessment

...

Arguments to pass to SS_output.

Details

Currently, the function uses values from the terminal year of the assessment for most life history parameters (growth, maturity, M, etc). Steepness values for the operating model are obtained by bootstrapping from spawning biomass and recruitment estimates in the assessment.

Value

An object of class OM.

Note

Currently supports the latest version of r4ss on CRAN (v.1.24). Function may be incompatible with newer versions of r4ss on Github.

Author(s)

T. Carruthers

See Also

SS2Data


MSEtool documentation built on Oct. 17, 2018, 9:04 a.m.