Management Strategy Evaluation Toolkit

Simulation tools for management strategy evaluation are provided for the 'DLMtool' operating model to inform data-rich fisheries. 'MSEtool' provides complementary assessment models of varying complexity with standardized reporting, diagnostic tools for evaluating assessment models within closed-loop simulation, and helper functions for building more complex operating models and management procedures.


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MSEtool is an extension of the DLMtool R package and provides simulation tools for management strategy evaluation informing data-rich fisheries. Find more information about DLMtool and MSEtool at http://datalimitedtoolkit.org/.

Installation

The released version of MSEtool can be downloaded from CRAN:

install.packages("MSEtool")

This GitHub repository contains the development version of MSEtool, which can be installed via:

devtools::install_github("tcarruth/MSEtool")

The development version may be unstable and it is typically not recommended for analyses.

User Guide

Vignettes describing the features of MSEtool can be obtained via:

browseVignettes("MSEtool")

A User Guide for the DLMtool package also available at https://dlmtool.github.io/DLMtool/userguide/introduction.html.

Bugs and Issues

Please report any bugs or issues through GitHub or the DLMtool website.

News


MSEtool 1.1.0

New additions, including:

  • Re-parameterization of dome selectivity in SCA so that estimated parameters are age-based after transformation.
  • Additional argument in SCA for lognormal distribution for age comps.
  • A more efficient method is used to report convergence diagnostics of assessment models when running in closed-loop simulation.

Minor edits, including:

  • By default, steepness is now fixed in the SCA and SCA2 assessment functions.
  • By default, nine data-rich MPs are now included in the package. See the help documentation: ?Data-rich-MP
  • A generic function for ramped harvest control rules (HCR_ramp) is now included. Users can input the desired limit and target reference points.
  • make_MP adds dependencies to the MP so that DLMtool::Required returns the appropriate dependencies. Dependencies are dynamic based on the configuration of the assessment model. For example, [email protected] is a dependency for a SCA-based model only if steepness is fixed.

MSEtool 1.0.0

  • Initial CRAN release.
  • Assessment models: Delay-Difference (DD_TMB, DD_SS); Surplus Production (SP, SP_SS); Statistical Catch-at-Age (SCA, SCA2)
  • Harvest control rules: HCR_MSY, HCR40_10, HCR60_20
  • simmov function for multiple-area movement models (age-independent)
  • Functions for converting Stock Synthesis and iSCAM assessments to OM and Data objects (classes inherited from DLMtool)

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("MSEtool")

1.1.0 by Tom Carruthers, 4 months ago


http://www.datalimitedtoolkit.org


Report a bug at https://github.com/tcarruth/MSEtool/issues


Browse source code at https://github.com/cran/MSEtool


Authors: Quang Huynh [aut] , Tom Carruthers [aut, cre] , Adrian Hordyk [aut] , Chris Grandin [ctb] (iSCAM functions)


Documentation:   PDF Manual  


GPL-3 license


Imports MASS, TMB, coda, corpcor, gplots, grDevices, graphics, methods, mvtnorm, pryr, r4ss, reshape2, snowfall, stats, utils

Depends on DLMtool

Suggests knitr, testthat

Linking to TMB, RcppEigen


See at CRAN