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MSEtool

The Management Strategy Evaluation toolkit (MSEtool) is the core package in the openMSE collection of packages. It contains the core functions for constructing operating models, simulating fishery dynamics, and evaluating the effectiveness of alternative management strategies using closed-loop simulation testing.

You can learn more about the openMSE packages at the openMSE documentation site.

Installation

You can install the released version of MSEtool from CRAN with:

install.packages("MSEtool")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("Blue-Matter/MSEtool")

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Version

Install

install.packages('MSEtool')

Monthly Downloads

459

Version

3.7.4

License

GPL-3

Maintainer

Adrian Hordyk

Last Published

June 4th, 2025

Functions in MSEtool (3.7.4)

Optimization function for CSRA

Catch at size reduction analysis

Internal function to create a blank plot for mapping selectivity at length

Identify management procedures (MPs) based on data availability

Check that specified MPs are valid and will run on MSEtool::SimulatedData

Check the years to summarize performance

Optimize for catchability (q)

Check OM object is complete

Manually map parameters for the historical period of operating model

Check for duplicated MPs names

Department of Fisheries and Oceans stock status bar plot

Department of Fisheries and Oceans historical plot

CalcMPDynamics_MF

Calculate population dynamics from MP recommendation for multi-fleet operating models

Calculate population dynamics from MP recommendation

CalcAsymptoticDist

Calculates the asymptotic distribution from an initial distribution vector (V) and a markov movement matrix (M) (rows sum to 1)

Current default thresholds for COSEWIC satisficing

Plot the median biomass and yield relative to last historical year

Department of Fisheries and Oceans projection plot

Department of Fisheries and Oceans biomass quantile plot

Create a standard DFO MSE report

Directory of the installed package on your computer

Create a standard DFO performance table

Atlantic_mackerel

Data class objects

DFO performance spider plot (top three MPs)

Converts a Data object into a .csv data file

Initialize Data Input Files

Determine dominate MPs

Read in Data object from Excel spreadsheet

Department of Fisheries and Oceans default plot 2

Department of Fisheries and Oceans trade-off plot

Directory of the data in the installed package on your computer

DataDescription

DataDescription

Class 'Fleet'

FleetDescription

FleetDescription

Check Convergence

DFO_tab_formatted

A formatted version of the standard DFO performance plot, color coded by thresholds

Create a blank MP recommendations object (class Rec) of the right dimensions

MP feasibility diagnostic

A flexible empirical management procedure.

Reference management procedures

Reconstruct historical dynamics

GenerateRandomWalk

Creates a time series per simulation that has a random normal walk with sigma

Function to run a set of input control methods

KOBE plot: a projection by projection plot of F/FMSY and B/BMSY

Fill any NAs arising from MPCalcs (hermaphroditism mode)

Depletion and F estimation from mean length of catches

HistDescription

HistDescription

Fleet class objects

Lag the time-series slots in a Data object by a specified number of time-steps

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

Imp class objects

National Oceanographic and Atmospheric Administration default plot 1

Length to age conversion

Internal function to calculate MSY Reference Points

Load more data from MSEextra package

Generate OM Documentation Report

Albacore_TwoFleet

MOM class objects

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

Internal Herm functions

Is a value NA or zero.

Replace an existing Stock, Fleet, Obs, or Imp object

Initialize Operating Model

Copy example OM XL and OM Documentation

A projection by projection plot of F/FMSY, B/BMSY, B/B0, and yield

MP feasibility diagnostic using real data

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

Reads data Stock Synthesis file structure into a nested Data object analogous with multiMSE

Generate a Data Report

OM class objects

Standardize values

Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet)

Make stochastic variables certain for only one rep

StockDescription

StockDescription

SampleStockPars

Sample Stock parameters

Class 'Stock'

Subset MSE object by management procedure (MP) or simulation.

Subset the cpars slot in an operating model

Current default thresholds for DFO satisficing

Sensitivity analysis

Management Procedure Type

Predict missing life-history parameters

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

Obs class objects

Subset a Stock, Fleet, Obs, or Imp object from an OM object

Performance Whisker Plot

Get help topic URL

Sample custom pars

Takes a fitted SAM model and samples historical population and fishing dynamics from the MLE fit and variance-covariance matrix.

Returns Results of a set of MICE relationships

An object for storing data for analysis using data-limited methods

Create a table of Performance Limits and Performance Objectives

Calculate TAC recommendations for more than one MP

Import a Data object from Excel file

PerformanceMetric

Performance Metrics Methods

Calculate Value Of Information 2

Calculate Probability

Yet another Value of Information Plot

Calculate Reference Yield

Boxplot of TAC recommendations

Get part of an MP specific data-list

Load OM from Excel file

Import Fleet Object from Excel file

SampleFleetPars

Sample Fleet Parameters

Sample Implementation Error Parameters

Blow parallel optimization function

Calculate Mean Probability

get object class

Standard MSE projection plot

What management procedures need what data

A projection by projection plot of F/FMSY and B/BMSY

genSizeCompWrap

Wrapper for C++ function to generate length composition

Calculate age at first capture from length at first capture and growth

Calculate parameters for beta distribution from mean and standard deviation in normal space

Sample Observation Parameters

Stock class objects

Combines indices into a single index using linear modelling (** Deprecated **)

Extract the first dimension of a hierarchical list of recommendation objects

initialize-methods

~~ Methods for Function initialize ~~

Stock recruit parameterization

Wrapper for histogram function

Utility functions for multiMSE objects

Apply Management Procedures to an object of class Data

Calculate Value Of Information

Find the Management Procedures that use a particular data slot

Internal function for checking that the OM@cpars is formatted correctly

Tom's expand grid

Class union for isRel slot

Utility functions for MSE objects

Generic Trade-Plot Function

Import Stock Object from Excel file

Join Data objects present in a list

Calculate CV from vector of values

Plot several plots with a shared legend

Plot Spawning stock biomass and reference points for both historical and projected period

Reads MPD or MCMC estimates and data from iSCAM file structure into an operating model

Rcpp version of the Optimization function that returns the squared difference between user specified and calculated movement parameters.

Combine data among fleets

Optimize yield for a single simulation

Combines all iSCAM age composition data across fleets

Plot Data object

Apply multi Management Procedures (class MMP) to a hierarchical list of Data class objects

Calculate selectivity curve

Combine data among stocks

A fairly tidy time-series quantile plot

getq_multi_MICE

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

Population dynamics model in CPP

Select DataList for an MP from MMSE@PPD

Get parameters of lognormal distribution from mean and standard deviation in normal space

SimulatedData Data

Internal wrapper function to calculate MSY reference points (now using MSYCalcs)

A basic SSB plot for debugging runMSE output

Plot a relationship between stocks

Calculates movement matrices from user inputs for fraction in each area (fracs) the relative fraction moving to other areas, plus a mean probability of staying in any given area.

Optimize q for a single simulation

General purpose polynomial smoother

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

Run a multi-fleet multi-stock Management Strategy Evaluation

Create indices that are sampled at various frequencies

What objects of this class are available

A quantile plot

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

Calculate a management recommendation given constraints

Optimization function to find a movement model that matches user specified movement characteristics modified for Rcpp.

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

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

Standard plot for an object of class MOM

Simulate Catch-at-Length Data

Simulate Catch-at-Age Data

Print out plotting functions

Apply the movement model to the stock for one time-step

Population dynamics for a MICE model (multiyear)

summary,Data-method

Summary of Data object

COSEWIC MSE run using the correct MPs and projected time horizon

Calculates movement matrices from user inputs

Enlarge (replicate) a DLM data object to create an additional dimension for simulation / sensitivity testing

A generic OFL plot for NOAA use

Calculates movement matrices from user specified distribution among other areas

Reads iSCAM files into a hierarchical R list object

Manually map the historical relative fishing effort trajectory.

Utility for making multi-OMs

Hockey Stick Harvest control rule that modifies TAC.

Double-normal selectivity curve

Calculate historical fishing mortality

Search R session for MP

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

makeTransparent

Make colors transparent

Dimensions of a hierarchical list object

Population dynamics for a MICE model (single year)

label.class-class

Label class union for performance metric objects

Valid custom parameters (cpars)

summary,MMSE-method

Summary of MMSE object

summary,MSE-method

Summary of MSE object

Remove observation, implementation, and process error

Lognormal distribution

Biomass wormplot

Internal function to write CSVs for objects

MICE relationships for multi-OM

Plot MSE object

Run a Management Strategy Evaluation

Plot Operating Model Object

Setup parallel processing

show,PMobj-method

Show the output of a PM

sample_steepness2

Sample steepness given mean and cv

Run a Management Procedure

Runs input control MPs on a Data object.

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

Determine optimal number of cpus

Show MSEtool S4 objects

prob.class-class

Prob class union for performance metric objects

Aging and Mortality for one time-step

show,Rec-method

Show the output of a single MP recommendation

Reads bootstrap estimates from a stock assessment model (including VPA) into an operating model. Assess2OM is identical to VPA2OM.

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

Import a multi-stock, multi-fleet OM from a BAM object

Reads bootstrap estimates from a stock assessment model into a multi-fleet operating model.

Convert ASAP 3 assessments into an operating model

Simplifies the CAL slot of data object

Blow internal parallel optimization function