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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

459

Version

1.3.0

License

GPL-3

Maintainer

Tom Carruthers

Last Published

October 1st, 2019

Functions in MSEtool (1.3.0)

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

Fill any NAs arising from MPCalcs (hermaphroditism mode)

MSEtool-package

Management Strategy Evaluation

Reads MLE estimates from CASAL file structure into an operating model

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

Calculates mahalanobis distance and rejection of the Null operating model

Statistical catch-at-age (SCA) model

Returns Results of a set of MICE relationships

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

Calculate MSY-based TAC from Assessment object

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

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

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

Compare output from several assessment models

Reads data from iSCAM file structure into a DLMtool Data object

optimize for catchability (q)

Albacore_TwoFleet

A two-fleet Albacore operating model

Make a custom management procedure (MP)

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

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

Data-rich management procedures

Reconstruct historical dynamics

Characterize posterior predictive data

Generic linear harvest control rule based on biomass

getq_multi_MICE

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

Plot SRA scope output

Plot profile object

Dimensions of a hierarchical list object

Combines indices into a single index using linear modelling

Plot stock-recruitment function

Run a multi-fleet multi-stock Management Strategy Evaluation

Plots probability distribution function of stock-recruit steepness

Reads iSCAM mcmc output files

Plots a beta variable

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

plot_timeseries

Plot time series of data

Reads iSCAM parameter file

Assessment-class

Class-Assessment

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

read.projection.file

Reads iSCAM projection file

Profile likelihood of assessment models

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

Find the production parameter based on depletion that produces MSY

Toms expand grid

Preliminary Assessments in MSE

Delay - Difference Stock Assessment in TMB

Rips MLE estimates from CASAL file structure

Virtual population analysis (VPA)

Reads MLE estimates from iSCAM file structure into an operating model

Combines all iSCAM age composition data across fleets

Combine data among fleets

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

Combine data among stocks

plot_lognormalvar

Plots a lognormal variable

Surplus production model with FMSY and MSY as leading parameters

What objects of this class are available

read.control.file

Reads iSCAM control file

Population dynamics for a MICE model (single year)

Population dynamics for a MICE model (multiyear)

summary.Assessment

Summary of Assessment object

North Atlantic Swordfish dataset

load.iscam.files

Reads iSCAM files into a hierarchical R list object

Continuous Delay-differential assessment model

Plot statistical power of the indicator with increasing time blocks

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

Reads iSCAM dat file

Get the MSEtool vignettes

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

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

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

Stock-reduction analysis (SRA) for conditioning operating models

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

read.report.file

Reads iSCAM Rep file

Standard plot for an object of class MOM

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

plot_composition

Plot composition data

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

fetch.file.names

Reads iSCAM Data, Control and Projection files

A basic SSB plot for debugging runMSE output

A fairly tidy time-series quantile plot

Optimize q for a single simulation

plot.Assessment

Plot Assessment object

retrospective_AM

retrospective_AM (retrospective of Assessment model in MSE)

Calculates movement matrices from user inputs

Plot a relationship between stocks

Methods for retro object

Retrospective analysis of assessment models

Linearly ramped harvest control rules