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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")

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.

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Version

Install

install.packages('MSEtool')

Monthly Downloads

704

Version

1.1.0

License

GPL-3

Maintainer

Tom Carruthers

Last Published

October 17th, 2018

Functions in MSEtool (1.1.0)

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

Calculate TAC from Assessment object

Make a custom management procedure (MP)

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

Plot statistical power of the indicator with increasing time blocks

summary,Assessment-method

Summary of Assessment object

plot_lognormalvar

Plots a lognormal variable

North Atlantic Swordfish dataset

Function that returns a stochastic estimate of steepness given observed stock recruitment data

Find the production parameter based on depletion that produces MSY

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

Reads data from iSCAM file structure into a DLMtool Data object

Characterize posterior predictive data

Extracts growth parameters from a SS3 r4ss replist

Predict recruitment and return fit to S-R observations

A function that samples multivariate normal (logspace) variables

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

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

Wrapper for estimating stock recruitment parameters from resampled stock-recruitment data

Calculates mahalanobis distance and rejection of the Null operating model

Reads MLE estimates from iSCAM file structure into an operating model

load.iscam.files

Reads iSCAM files into a hierarchical R list object

Combines indices into a single index using linear modelling

Ramped harvest control rules

Combines all iSCAM age composition data across fleets

Generic linear harvest control rule based on biomass

Statistical catch-at-age (SCA) model

plot_timeseries

Plot time series of data

Simplified a multi-area transition matrix into the best 2 x 2 representation

Reads iSCAM parameter file

Preliminary Assessments in MSE

Surplus production model with UMSY and MSY as leading parameters

Reads iSCAM dat file

Reads iSCAM mcmc output files

read.projection.file

Reads iSCAM projection file

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

plot,Assessment,ANY-method

Plot Assessment object

Plot stock-recruitment function

fetch.file.names

Reads iSCAM Data, Control and Projection files

plot_composition

Plot composition data

Plots a beta variable

profile_likelihood

Profile likelihood of assessment models

read.control.file

Reads iSCAM control file

retrospective_AM

retrospective_AM (retrospective of Assessment model in MSE)

Calculates movement matrices from user inputs

Plots probability distribution function of stock-recruit steepness

read.report.file

Reads iSCAM Rep file

Retrospective analysis of assessment models

Assessment-class

Class-Assessment

Delay - Difference Stock Assessment in TMB

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

Linear interpolation of a y value at level xlev based on a vector x and y

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

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

MSEtool-package

Management Strategy Evaluation

Data-rich management procedures

What objects of this class are available