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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

693

Version

3.1.0

License

GPL-3

Maintainer

Adrian Hordyk

Last Published

July 3rd, 2021

Functions in MSEtool (3.1.0)

Simplifies the CAL slot of data object

Optimization function for CSRA

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

Check for duplicated MPs names

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

Calculate population dynamics from MP recommendation

Optimize for catchability (q)

Catch at size reduction analysis

Blow internal parallel optimization function

Department of Fisheries and Oceans trade-off plot

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

Department of Fisheries and Oceans historical plot

Department of Fisheries and Oceans stock status bar plot

Identify management procedures (MPs) based on data availability

Current default thresholds for COSEWIC satisficing

DFO performance spider plot (top three MPs)

Create a standard DFO MSE report

Check Convergence

Converts a Data object into a .csv data file

Fleet class objects

Class 'Fleet'

DFO_tab_formatted

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

Directory of the data in the installed package on your computer

DataDescription

DataDescription

Create a standard DFO performance table

Plot the median biomass and yield relative to last historical year

Directory of the installed package on your computer

MP feasibility diagnostic

Atlantic_mackerel

Data class objects

Read in Data object from Excel spreadsheet

Manually map parameters for the historical period of operating model

Reconstruct historical dynamics

Determine dominate MPs

Check the years to summarize performance

Imp class objects

Length to age conversion

Department of Fisheries and Oceans default plot 2

Initialize Data Input Files

FleetDescription

FleetDescription

Predict missing life-history parameters

Internal function to calculate MSY Reference Points

Function to run a set of input control methods

Reference management procedures

GenerateRandomWalk

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

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

Fill any NAs arising from MPCalcs (hermaphroditism mode)

HistDescription

HistDescription

OM class objects

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

Management Procedure Type

Sensitivity analysis

Generate a Data Report

Copy example OM XL and OM Documentation

Department of Fisheries and Oceans projection plot

SimulatedData Data

Get help topic URL

Initialize Operating Model

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

Department of Fisheries and Oceans biomass quantile plot

Is a value NA or zero.

MP feasibility diagnostic using real data

Standardize values

Load more data from MSEextra package

Make stochastic variables certain for only one rep

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

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

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

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

Depletion and F estimation from mean length of catches

Calculate TAC recommendations for more than one MP

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

Obs class objects

Subset an OM cpars slot

Sample Implementation Error Parameters

SampleStockPars

Sample Stock parameters

Boxplot of TAC recommendations

Calculate Value Of Information 2

Calculate Value Of Information

SampleFleetPars

Sample Fleet Parameters

Sample custom pars

Calculate Mean Probability

Sample Observation Parameters

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

Albacore_TwoFleet

MOM class objects

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

Class 'Stock'

Plot Operating Model Object

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

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

read.control.file

Reads iSCAM control file

Print out plotting functions

Yet another Value of Information Plot

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

StockDescription

StockDescription

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

Generic Trade-Plot Function

Calculate Probability

Import a Data object from Excel file

Current default thresholds for DFO satisficing

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

Calculate Reference Yield

summary,Data-method

Summary of Data object

Runs input control MPs on a Data object.

COSEWIC MSE run using the correct MPs and projected time horizon

getq_multi_MICE

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

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

Get part of an MP specific data-list

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

National Oceanographic and Atmospheric Administration default plot 1

Calculate historical fishing mortality

Plot MSE object

Reads data from iSCAM file structure into a Data object

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

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

A fairly tidy time-series quantile plot

show,Rec-method

Show the output of a single MP recommendation

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

read.report.file

Reads iSCAM Rep file

Population dynamics model in CPP

summary,MSE-method

Summary of MSE object

Generate OM Documentation Report

Remove observation, implementation, and process error

Simulate Catch-at-Age Data

Lognormal distribution for DLMtool

initialize-methods

~~ Methods for Function initialize ~~

Optimize q for a single simulation

label.class-class

Label class union for performance metric objects

Dimensions of a hierarchical list object

Combines indices into a single index using linear modelling

Import Fleet Object from Excel file

Aging and Mortality for one time-step

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

Create a table of Performance Limits and Performance Objectives

Performance Whisker Plot

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

prob.class-class

Prob class union for performance metric objects

Calculates movement matrices from user inputs

Reads iSCAM parameter file

PerformanceMetric

Performance Metrics Methods

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

Manually map the historical relative fishing effort trajectory.

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

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

read.projection.file

Reads iSCAM projection file

Simulate Catch-at-Length Data

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

Double-normal selectivity curve

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

Stock class objects

Find the Management Procedures that use a particular data slot

Import Stock Object from Excel file

Load OM from Excel file

Calculate CV from vector of values

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

fetch.file.names

Reads iSCAM Data, Control and Projection files

genSizeCompWrap

Wrapper for C++ function to generate length composition

Blow parallel optimization function

Combines all iSCAM age composition data across fleets

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

Reads MLE estimates from iSCAM file structure into an operating model

Plot several plots with a shared legend

Join Data objects present in a list

What management procedures need what data

Returns Results of a set of MICE relationships

Run a multi-fleet multi-stock Management Strategy Evaluation

Combine data among stocks

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

Population dynamics for a MICE model (multiyear)

Determine optimal number of cpus

Setup parallel processing

Population dynamics for a MICE model (single year)

Combine data among fleets

show,PMobj-method

Show the output of a PM

Internal function to write CSVs for objects

Tom's expand grid

What objects of this class are available

Apply Management Procedures to an object of class Data

Class union for isRel slot

Run a Management Procedure

Run a Management Strategy Evaluation

sample_steepness2

Sample steepness given mean and cv

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

Valid custom parameters (cpars)

get object class

Extract the first dimension of a hierarchical list of recommendation objects

Utility functions for MSE objects

Biomass wormplot

makeTransparent

Make colors transparent

Wrapper for histogram function

Plot Data object

Calculate selectivity curve

load.iscam.files

Reads iSCAM files into a hierarchical R list object

Optimize yield for a single simulation

A generic OFL plot for NOAA use

Reads iSCAM mcmc output files

Reads iSCAM dat file

A basic SSB plot for debugging runMSE output