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.


CRAN_Status_Badge

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")

1.3.0 by Tom Carruthers, 21 days 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, reshape2, snowfall, stats, utils, abind, rmarkdown

Depends on DLMtool

Suggests knitr, testthat, r4ss, shiny

Linking to TMB, RcppEigen


See at CRAN