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MSEtool

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")

The 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")

The vignettes can also be viewed on the MSEtool page on CRAN.

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.

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Version

Install

install.packages('MSEtool')

Monthly Downloads

704

Version

1.5.0

License

GPL-3

Maintainer

Tom Carruthers

Last Published

March 24th, 2020

Functions in MSEtool (1.5.0)

Reads MCMC estimates from Awatea (Paul Starr) processed r file structure into an operating model

Rips MLE estimates from CASAL file structure

Data-rich management procedures

Harvest control rule to fish at some fraction of maximum sustainable yield

A Harvest Control Rule using B/BMSY and F/FMSY to adjust TAC or TAE.

Albacore_TwoFleet

A two-fleet Albacore operating model

Delay - Difference Stock Assessment in TMB

Linearly ramped harvest control rules

Reads MLE estimates from CASAL file structure into an operating model

Assessment-class

Class-Assessment

Item in list: get the list values from a list of lists

Calculates mahalanobis distance and rejection of the Null operating model

Calculate mahalanobis distance (null and alternative MSEs) and statistical power for all MPs in an MSE

Generic linear harvest control rule based on biomass

Returns Results of a set of MICE relationships

Fill any NAs arising from MPCalcs (hermaphroditism mode)

What objects of this class are available

Surplus production model with FMSY and MSY as leading parameters

Continuous Delay-differential assessment model

Sum over list: get the list values from a list of lists

Reconstruct historical dynamics

Expand the Herm list in SexPars to a matrix of fractions at age

Find the production parameter based on depletion that produces MSY

Make a custom management procedure (MP)

Calculates movement matrices from user inputs for fraction in each area (fracs) and probability of staying in areas (prob)

Reads data from iSCAM file structure into a DLMtool Data object

plot_lognormalvar

Plots a lognormal variable

Calculate MSY-based TAC from Assessment object

fetch.file.names

Reads iSCAM Data, Control and Projection files

MSEtool-package

Management Strategy Evaluation

Reads MLE estimates from Stock Synthesis file structure into an operating model using package r4ss.

Stock-reduction analysis (SRA) for conditioning operating models

Reads data Stock Synthesis file structure into a Data object using package r4ss

Toms expand grid

Statistical catch-at-age (SCA) model

Virtual population analysis (VPA)

Combines indices into a single index using linear modelling

Characterize posterior predictive data

Derives the rate of exchange from one sex to another based on asymptotic fraction

Slot in list: get the slot values from a list of objects

Dimensions of a hierarchical list object

Compare output from several assessment models

Reads MLE estimates from iSCAM file structure into an operating model

diagnostic_AM (diagnostic of Assessments in MSE): Did Assess models converge during MSE?

load.iscam.files

Reads iSCAM files into a hierarchical R list object

plot.Assessment

Plot Assessment object

Combines all iSCAM age composition data across fleets

Optimize q for a single simulation

Plot statistical power of the indicator with increasing time blocks

Plot a relationship between stocks

Methods for retro object

Combine data among fleets

Combine data among stocks

A basic SSB plot for debugging runMSE output

Plot SRA scope output

A fairly tidy time-series quantile plot

plot_timeseries

Plot time series of data

Plots probability distribution function of stock-recruit steepness

read.control.file

Reads iSCAM control file

Plot profile object

Preliminary Assessments in MSE

Projections for assessment models

Standard plot for an object of class MOM

Count independent variables for a MICE relationship at position x in a Rel list

Standard plot for an object of class MMSE (multi MSE)

Reads iSCAM dat file

getq_multi_MICE

optimize for catchability (q) and fishing dist for a MICE model

retrospective_AM

retrospective_AM (retrospective of Assessment model in MSE)

plot_composition

Plot composition data

Calculates movement matrices from user inputs

Retrospective analysis of assessment models

Run a multi-fleet multi-stock Management Strategy Evaluation

Produce a cross-correlation plot of the derived data arising from getinds(MSE_object)

Population dynamics for a MICE model (multiyear)

optimize for catchability (q)

Plot stock-recruitment function

read.projection.file

Reads iSCAM projection file

A basic comparison of runMSE output (MSE) and multiMSE (MMSE)

read.report.file

Reads iSCAM Rep file

summary.Assessment

Summary of Assessment object

Plots a beta variable

Profile likelihood of assessment models

Class-project

North Atlantic Swordfish dataset

Internal function for optimizing catchability (q) for a MICE model

Reads iSCAM mcmc output files

Reads iSCAM parameter file

Get the MSEtool vignettes

Population dynamics for a MICE model (single year)

Remove observation error, process error, implementation error or future gradients in (time varying) parameters