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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:

devtools::install_github("tcarruth/MSEtool", build_vignettes = TRUE)
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

693

Version

2.0.0

License

GPL-3

Maintainer

Tom Carruthers

Last Published

August 6th, 2020

Functions in MSEtool (2.0.0)

Rips MLE estimates from CASAL file structure

Linearly ramped harvest control rules

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

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

Generic linear harvest control rule based on biomass

Albacore_TwoFleet

A two-fleet Albacore operating model

Reads MLE estimates from CASAL file structure into an operating model

Delay - Difference Stock Assessment in TMB

Assessment-class

Class-Assessment

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

Reconstruct historical dynamics

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

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

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

Stock-reduction analysis (SRA) for conditioning operating models

Find the production parameter based on depletion that produces MSY

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

Calculates mahalanobis distance and rejection of the Null operating model

Returns Results of a set of MICE relationships

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

Dimensions of a hierarchical list object

Continuous Delay-differential assessment model

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

Fill any NAs arising from MPCalcs (hermaphroditism mode)

MSEtool-package

Management Strategy Evaluation

Combines indices into a single index using linear modelling

Combines all iSCAM age composition data across fleets

fetch.file.names

Reads iSCAM Data, Control and Projection files

Characterize posterior predictive data

Simple Stock Synthesis

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

Reads MLE estimates from iSCAM file structure into an operating model

Reads data from iSCAM file structure into a DLMtool Data object

Combine data among fleets

Compare output from several assessment models

Model-based management procedures

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

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

optimize for catchability (q)

Statistical catch-at-age (SCA) model

Plot profile object

Virtual population analysis (VPA)

What objects of this class are available

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

Methods for retro object

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

plot.Assessment

Plot Assessment object

plot_timeseries

Plot time series of data

Population dynamics for a MICE model (single year)

Optimize q for a single simulation

Standard plot for an object of class MOM

Reads iSCAM dat file

A basic SSB plot for debugging runMSE output

Reads iSCAM mcmc output files

A fairly tidy time-series quantile plot

Class-project

plot_composition

Plot composition data

Plots a beta variable

Population dynamics for a MICE model (multiyear)

Preliminary Assessments in MSE

load.iscam.files

Reads iSCAM files into a hierarchical R list object

Plot SRA scope output

Plot statistical power of the indicator with increasing time blocks

Retrospective analysis of assessment models

Toms expand grid

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

Run a multi-fleet multi-stock Management Strategy Evaluation

Surplus production model with FMSY and MSY as leading parameters

Calculate MSY-based TAC from Assessment object

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

Combine data among stocks

retrospective_AM

retrospective_AM (retrospective of Assessment model in MSE)

getq_multi_MICE

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

Make a custom management procedure (MP)

summary.Assessment

Summary of Assessment object

Plots probability distribution function of stock-recruit steepness

read.projection.file

Reads iSCAM projection file

plot_lognormalvar

Plots a lognormal variable

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

Reads iSCAM parameter file

Calculates movement matrices from user inputs

Plot a relationship between stocks

read.control.file

Reads iSCAM control file

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

North Atlantic Swordfish dataset

read.report.file

Reads iSCAM Rep file

Profile likelihood of assessment models

Plot stock-recruitment function

Projections for assessment models

Get the MSEtool vignettes

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