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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 https://www.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

397

Version

2.0.1

License

GPL-3

Maintainer

Tom Carruthers

Last Published

September 29th, 2020

Functions in MSEtool (2.0.1)

Assessment-class

Class-Assessment

Delay - Difference Stock Assessment in TMB

Rips MLE estimates from CASAL file structure

Albacore_TwoFleet

A two-fleet Albacore operating model

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

Reads MLE estimates from CASAL file structure into an operating model

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

Calculates mahalanobis distance and rejection of the Null operating model

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

Linearly ramped harvest control rules

Returns Results of a set of MICE relationships

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

Reconstruct historical dynamics

Fill any NAs arising from MPCalcs (hermaphroditism mode)

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

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

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

Generic linear harvest control rule based on biomass

Stock-reduction analysis (SRA) for conditioning operating models

MSEtool-package

Management Strategy Evaluation

Model-based management procedures

Statistical catch-at-age (SCA) model

Import Stock Synthesis to multi-fleet 2-sex MOM

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

Find the production parameter based on depletion that produces MSY

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

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

optimize for catchability (q)

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

Plot profile object

Methods for retro object

Optimize q for a single simulation

A fairly tidy time-series quantile plot

Continuous Delay-differential assessment model

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

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

Surplus production model with FMSY and MSY as leading parameters

Reads data from iSCAM file structure into a DLMtool Data object

Simple Stock Synthesis

Calculate MSY-based TAC from Assessment object

fetch.file.names

Reads iSCAM Data, Control and Projection files

Population dynamics for a MICE model (multiyear)

Characterize posterior predictive data

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

Compare output from several assessment models

Combine data among stocks

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

getq_multi_MICE

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

Virtual population analysis (VPA)

Reads MLE estimates from iSCAM file structure into an operating model

Toms expand grid

Combines all iSCAM age composition data across fleets

Combines indices into a single index using linear modelling

Plot statistical power of the indicator with increasing time blocks

Plots a beta variable

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

Reads bootstrap estimates from a VPA stock assessment into an operating model.

Run a multi-fleet multi-stock Management Strategy Evaluation

plot_composition

Plot composition data

Combine data among fleets

read.control.file

Reads iSCAM control file

Calculates movement matrices from user inputs

Retrospective analysis of assessment models

Make a custom management procedure (MP)

retrospective_AM

retrospective_AM (retrospective of Assessment model in MSE)

Plot a relationship between stocks

plot.Assessment

Plot Assessment object

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

What objects of this class are available

A basic SSB plot for debugging runMSE output

Reads iSCAM dat file

plot_timeseries

Plot time series of data

Dimensions of a hierarchical list object

Plot stock-recruitment function

summary.Assessment

Summary of Assessment object

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

Projections for assessment models

Class-project

Plots probability distribution function of stock-recruit steepness

load.iscam.files

Reads iSCAM files into a hierarchical R list object

Plot SRA scope output

plot_lognormalvar

Plots a lognormal variable

Standard plot for an object of class MOM

Get the MSEtool vignettes

Reads iSCAM mcmc output files

Population dynamics for a MICE model (single year)

Reads iSCAM parameter file

read.projection.file

Reads iSCAM projection file

Preliminary Assessments in MSE

North Atlantic Swordfish dataset

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

Profile likelihood of assessment models

read.report.file

Reads iSCAM Rep file