ss3om

Overview

Tools for loading Stock Synthesis (SS3) models into FLR. Used in conditioning of Operating Models based on SS3 by considering structural uncertainty in input parameters and assumptions. A grid of SS3 runs can be created and results loaded on objects of various classes, ready for use in FLR.

Installation

To install this package, and all its dependencies, start R and enter:

  install.packages("ss3om", repos=structure(
    c(CRAN="https://cloud.r-project.org/", FLR="https://flr-project.org/R")))

or directly from the github repository by first updating to the latest version of r4ss:

  remotes::install_github("r4ss/r4ss")
  remotes::install_github("flr/ss3om")

Usage

Different FLR objects can be loaded from a folder containing the output of an SS3 run.

dir <- system.file("ext-data", "herring", package="ss3om")

To create an FLStock object from a model run, we can call readFLSss3,

stk <- readFLSss3(dir)

plot(stk)

stk

and to extract and convert the stock-recruit relationship, you can use

srr <- readFLSRss3(dir)

plot(her)

srr

License

Copyright (c) 2016-2022 European Union & Iago Mosqueira. Released under the EUPL 1.2.

Contact

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