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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

397

Version

3.7.3

License

GPL-3

Maintainer

Adrian Hordyk

Last Published

November 22nd, 2024

Functions in MSEtool (3.7.3)

Check for duplicated MPs names

Optimize for catchability (q)

Check OM object is complete

CalcAsymptoticDist

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

Calculate population dynamics from MP recommendation

Identify management procedures (MPs) based on data availability

Check the years to summarize performance

Manually map parameters for the historical period of operating model

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

Department of Fisheries and Oceans biomass quantile plot

Department of Fisheries and Oceans historical plot

Department of Fisheries and Oceans trade-off plot

Check Convergence

DFO performance spider plot (top three MPs)

Current default thresholds for COSEWIC satisficing

Create a standard DFO performance table

Department of Fisheries and Oceans projection plot

Initialize Data Input Files

Department of Fisheries and Oceans default plot 2

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

Department of Fisheries and Oceans stock status bar plot

Plot the median biomass and yield relative to last historical year

Create a standard DFO MSE report

Atlantic_mackerel

Data class objects

Converts a Data object into a .csv data file

Reference management procedures

MP feasibility diagnostic

DataDescription

DataDescription

DFO_tab_formatted

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

Internal Herm functions

Directory of the installed package on your computer

FleetDescription

FleetDescription

Fleet class objects

Class 'Fleet'

Fill any NAs arising from MPCalcs (hermaphroditism mode)

Read in Data object from Excel spreadsheet

Depletion and F estimation from mean length of catches

Determine dominate MPs

Directory of the data in the installed package on your computer

Reconstruct historical dynamics

HistDescription

HistDescription

GenerateRandomWalk

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

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

Load more data from MSEextra package

National Oceanographic and Atmospheric Administration default plot 1

Management Procedure Type

A flexible empirical management procedure.

Function to run a set of input control methods

Albacore_TwoFleet

MOM class objects

Imp class objects

Initialize Operating Model

Is a value NA or zero.

Copy example OM XL and OM Documentation

Internal function to calculate MSY Reference Points

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

Predict missing life-history parameters

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

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

Performance Whisker Plot

Obs class objects

PerformanceMetric

Performance Metrics Methods

What management procedures need what data

Length to age conversion

Returns Results of a set of MICE relationships

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

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

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

StockDescription

StockDescription

SampleFleetPars

Sample Fleet Parameters

Create a table of Performance Limits and Performance Objectives

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

Get help topic URL

Generate a Data Report

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

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

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

Tom's expand grid

Standardize values

Manually map the historical relative fishing effort trajectory.

Standard MSE projection plot

Generate OM Documentation Report

OM class objects

Import Stock Object from Excel file

Load OM from Excel file

Import a Data object from Excel file

Calculate TAC recommendations for more than one MP

Calculate Value Of Information 2

Sample Implementation Error Parameters

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

Import Fleet Object from Excel file

Generic Trade-Plot Function

Current default thresholds for DFO satisficing

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

Yet another Value of Information Plot

Stock class objects

Sample custom pars

Calculate Value Of Information

Calculate Probability

genSizeCompWrap

Wrapper for C++ function to generate length composition

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

Utility functions for MSE objects

Class union for isRel slot

Class 'Stock'

Get part of an MP specific data-list

Calculate Reference Yield

Blow parallel optimization function

getq_multi_MICE

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

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

Join Data objects present in a list

Plot several plots with a shared legend

Make stochastic variables certain for only one rep

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

Double-normal selectivity curve

Calculate CV from vector of values

Hockey Stick Harvest control rule that modifies TAC.

Run a multi-fleet multi-stock Management Strategy Evaluation

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

Subset the cpars slot in an operating model

Sample Observation Parameters

SampleStockPars

Sample Stock parameters

Dimensions of a hierarchical list object

Wrapper for histogram function

Stock recruit parameterization

Combine data among stocks

Calculate selectivity curve

Combines all iSCAM age composition data across fleets

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

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

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

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

Optimize q for a single simulation

Apply Management Procedures to an object of class Data

Calculate a management recommendation given constraints

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

What objects of this class are available

Create indices that are sampled at various frequencies

Utility for making multi-OMs

makeTransparent

Make colors transparent

MICE relationships for multi-OM

Population dynamics for a MICE model (single year)

label.class-class

Label class union for performance metric objects

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

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

Sensitivity analysis

MP feasibility diagnostic using real data

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.

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

Population dynamics for a MICE model (multiyear)

Plot Operating Model Object

Standard plot for an object of class MOM

Reads iSCAM files into a hierarchical R list object

A generic OFL plot for NOAA use

Print out plotting functions

SimulatedData Data

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

Determine optimal number of cpus

Run a Management Procedure

Plot a relationship between stocks

General purpose polynomial smoother

sample_steepness2

Sample steepness given mean and cv

Run a Management Strategy Evaluation

Find the Management Procedures that use a particular data slot

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

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

Plot MSE object

initialize-methods

~~ Methods for Function initialize ~~

summary,Data-method

Summary of Data object

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

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

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

Remove observation, implementation, and process error

COSEWIC MSE run using the correct MPs and projected time horizon

A quantile plot

Lognormal distribution

Calculates movement matrices from user specified distribution among other areas

Runs input control MPs on a Data object.

Valid custom parameters (cpars)

Calculates movement matrices from user inputs

Select DataList for an MP from MMSE@PPD

Calculate historical fishing mortality

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

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

Boxplot of TAC recommendations

Combine data among fleets

get object class

Search R session for MP

Calculate Mean Probability

Extract the first dimension of a hierarchical list of recommendation objects

Aging and Mortality for one time-step

Optimize yield for a single simulation

Setup parallel processing

Simulate Catch-at-Length Data

Internal function to write CSVs for objects

prob.class-class

Prob class union for performance metric objects

A fairly tidy time-series quantile plot

Plot Data object

Population dynamics model in CPP

show,PMobj-method

Show the output of a PM

Simulate Catch-at-Age Data

summary,MMSE-method

Summary of MMSE object

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

A basic SSB plot for debugging runMSE output

show,Rec-method

Show the output of a single MP recommendation

Show MSEtool S4 objects

summary,MSE-method

Summary of MSE object

Biomass wormplot

Convert ASAP 3 assessments into an operating model

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

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

Optimization function for CSRA

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

Catch at size reduction analysis

Blow internal parallel optimization function

Simplifies the CAL slot of data object

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

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