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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

3.1.1

License

GPL-3

Maintainer

Adrian Hordyk

Last Published

July 8th, 2021

Functions in MSEtool (3.1.1)

Blow internal parallel optimization function

Optimize for catchability (q)

Catch at size reduction analysis

Identify management procedures (MPs) based on data availability

Simplifies the CAL slot of data object

Check for duplicated MPs names

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

Optimization function for CSRA

Calculate population dynamics from MP recommendation

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

Check the years to summarize performance

Department of Fisheries and Oceans historical plot

Department of Fisheries and Oceans stock status bar plot

Manually map parameters for the historical period of operating model

Department of Fisheries and Oceans default plot 2

Department of Fisheries and Oceans biomass quantile plot

Department of Fisheries and Oceans trade-off plot

Department of Fisheries and Oceans projection plot

Directory of the installed package on your computer

Atlantic_mackerel

Data class objects

DFO performance spider plot (top three MPs)

Create a standard DFO MSE report

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

Fleet class objects

Check Convergence

Converts a Data object into a .csv data file

Class 'Fleet'

Plot the median biomass and yield relative to last historical year

Current default thresholds for COSEWIC satisficing

Reference management procedures

Function to run a set of input control methods

Determine dominate MPs

FleetDescription

FleetDescription

Read in Data object from Excel spreadsheet

HistDescription

HistDescription

Depletion and F estimation from mean length of catches

Initialize Data Input Files

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

Create a standard DFO performance table

DFO_tab_formatted

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

Load more data from MSEextra package

Imp class objects

Directory of the data in the installed package on your computer

OM class objects

Albacore_TwoFleet

MOM class objects

Reconstruct historical dynamics

DataDescription

DataDescription

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

Get help topic URL

GenerateRandomWalk

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

Fill any NAs arising from MPCalcs (hermaphroditism mode)

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

PerformanceMetric

Performance Metrics Methods

Management Procedure Type

Is a value NA or zero.

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

Internal function to calculate MSY Reference Points

Performance Whisker Plot

Obs class objects

Create a table of Performance Limits and Performance Objectives

MP feasibility diagnostic

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

Subset an OM cpars slot

Sample custom pars

Tom's expand grid

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

Manually map the historical relative fishing effort trajectory.

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

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

Stock class objects

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

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

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

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

SampleFleetPars

Sample Fleet Parameters

Generate OM Documentation Report

Sample Implementation Error Parameters

StockDescription

StockDescription

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

Calculate Mean Probability

Get part of an MP specific data-list

Boxplot of TAC recommendations

Yet another Value of Information Plot

Find the Management Procedures that use a particular data slot

Class 'Stock'

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

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

Make stochastic variables certain for only one rep

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

Standardize values

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

Utility functions for MSE objects

getq_multi_MICE

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

Wrapper for histogram function

Combine data among fleets

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

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

Calculate selectivity curve

Class union for isRel slot

MP feasibility diagnostic using real data

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

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

Join Data objects present in a list

Plot several plots with a shared legend

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

Calculate historical fishing mortality

Plot Data object

Predict missing life-history parameters

Length to age conversion

Optimize yield for a single simulation

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

read.control.file

Reads iSCAM control file

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

National Oceanographic and Atmospheric Administration default plot 1

Copy example OM XL and OM Documentation

Blow parallel optimization function

Generate a Data Report

Initialize Operating Model

Reads iSCAM dat file

Reads iSCAM mcmc output files

Calculate TAC recommendations for more than one MP

Import Stock Object from Excel file

Calculate Probability

Load OM from Excel file

Plot MSE object

A fairly tidy time-series quantile plot

What management procedures need what data

Returns Results of a set of MICE relationships

Sensitivity analysis

Calculate Reference Yield

SimulatedData Data

Calculate Value Of Information 2

Calculate Value Of Information

Import a Data object from Excel file

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

Import Fleet Object from Excel file

show,Rec-method

Show the output of a single MP recommendation

Simulate Catch-at-Age Data

genSizeCompWrap

Wrapper for C++ function to generate length composition

Plot Operating Model Object

Combines indices into a single index using linear modelling

initialize-methods

~~ Methods for Function initialize ~~

fetch.file.names

Reads iSCAM Data, Control and Projection files

Current default thresholds for DFO satisficing

Population dynamics model in CPP

SampleStockPars

Sample Stock parameters

Sample Observation Parameters

Reads MLE estimates from iSCAM file structure into an operating model

Calculate CV from vector of values

Reads iSCAM parameter file

sample_steepness2

Sample steepness given mean and cv

read.projection.file

Reads iSCAM projection file

Remove observation, implementation, and process error

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

Apply Management Procedures to an object of class Data

Generic Trade-Plot Function

Extract the first dimension of a hierarchical list of recommendation objects

get object class

Combines all iSCAM age composition data across fleets

Combine data among stocks

Run a multi-fleet multi-stock Management Strategy Evaluation

Reads data from iSCAM file structure into a Data object

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

A basic SSB plot for debugging runMSE output

Print out plotting functions

A generic OFL plot for NOAA use

Lognormal distribution for DLMtool

makeTransparent

Make colors transparent

Optimize q for a single simulation

load.iscam.files

Reads iSCAM files into a hierarchical R list object

Run a Management Procedure

read.report.file

Reads iSCAM Rep file

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

Setup parallel processing

Run a Management Strategy Evaluation

show,PMobj-method

Show the output of a PM

What objects of this class are available

Biomass wormplot

Valid custom parameters (cpars)

Simulate Catch-at-Length Data

Aging and Mortality for one time-step

Calculates movement matrices from user inputs

prob.class-class

Prob class union for performance metric objects

Double-normal selectivity curve

Dimensions of a hierarchical list object

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

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

Internal function to write CSVs for objects

label.class-class

Label class union for performance metric objects

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

Determine optimal number of cpus

Population dynamics for a MICE model (multiyear)

Population dynamics for a MICE model (single year)

Runs input control MPs on a Data object.

COSEWIC MSE run using the correct MPs and projected time horizon

summary,Data-method

Summary of Data object

summary,MSE-method

Summary of MSE object