Learn R Programming

⚠️There's a newer version (3.7.5) of this package.Take me there.

MSEtool V3.0.0

This is a new major release of the MSEtool package. It is not backwards compatible with previous versions of MSEtool or DLMtool.

This README will be updated when the package is released on CRAN.

Copy Link

Version

Install

install.packages('MSEtool')

Monthly Downloads

693

Version

3.0.0

License

GPL-3

Maintainer

Adrian Hordyk

Last Published

January 9th, 2021

Functions in MSEtool (3.0.0)

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

Identify management procedures (MPs) based on data availability

Check for duplicated MPs names

Simplifies the CAL slot of data object

Optimization function for CSRA

Blow internal parallel optimization function

Catch at size reduction analysis

Optimize for catchability (q)

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

Calculate population dynamics from MP recommendation

Current default thresholds for COSEWIC satisficing

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

Check the years to summarize performance

Atlantic_mackerel

Data class objects

MP feasibility diagnostic

Reference management procedures

Directory of the installed package on your computer

Department of Fisheries and Oceans historical plot

Create a standard DFO MSE report

Department of Fisheries and Oceans stock status bar plot

DFO performance spider plot (top three MPs)

Plot the median biomass and yield relative to last historical year

Manually map parameters for the historical period of operating model

Create a standard DFO performance table

Read in Data object from Excel spreadsheet

DFO_tab_formatted

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

Initialize Data Input Files

Depletion and F estimation from mean length of catches

Length to age conversion

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

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

Is a value NA or zero.

Determine dominate MPs

Imp class objects

Initialize Operating Model

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

Converts a Data object into a .csv data file

Fleet class objects

Check Convergence

Class 'Fleet'

Directory of the installed package on your computer

Create a table of Performance Limits and Performance Objectives

MP feasibility diagnostic using real data

Obs class objects

Reconstruct historical dynamics

Make stochastic variables certain for only one rep

DataDescription

DataDescription

Department of Fisheries and Oceans trade-off plot

Sample custom pars

Predict missing life-history parameters

StockDescription

StockDescription

SampleFleetPars

Sample Fleet Parameters

Import a Data object from Excel file

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

Calculate Reference Yield

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

getq_multi_MICE

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

Department of Fisheries and Oceans default plot 2

Class union for isRel slot

Department of Fisheries and Oceans biomass quantile plot

Department of Fisheries and Oceans projection plot

Function to run a set of input control methods

Management Procedure Type

Subset an OM cpars slot

Get help topic URL

National Oceanographic and Atmospheric Administration default plot 1

Load more data from MSEextra package

Albacore_TwoFleet

MOM class objects

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

Reads data from iSCAM file structure into a Data object

Calculate selectivity curve

Reads MLE estimates from iSCAM file structure into an operating model

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

Standardize values

FleetDescription

FleetDescription

GenerateRandomWalk

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

Sensitivity analysis

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

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

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

SampleStockPars

Sample Stock parameters

Optimize q for a single simulation

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

Internal function to calculate MSY Reference Points

Calculate Value Of Information 2

OM class objects

PerformanceMetric

Performance Metrics Methods

Calculate Value Of Information

Find the Management Procedures that use a particular data slot

What objects of this class are available

Yet another Value of Information Plot

read.control.file

Reads iSCAM control file

Optimize yield for a single simulation

Reads iSCAM dat file

Copy example OM XL and OM Documentation

Generate OM Documentation Report

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

Calculate historical fishing mortality

Run a multi-fleet multi-stock Management Strategy Evaluation

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

fetch.file.names

Reads iSCAM Data, Control and Projection files

Boxplot of TAC recommendations

get object class

initialize-methods

~~ Methods for Function initialize ~~

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

What management procedures need what data

COSEWIC MSE run using the correct MPs and projected time horizon

Simulate Catch-at-Length Data

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

Simulate Catch-at-Age Data

Plot Data object

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

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

Fill any NAs arising from MPCalcs (hermaphroditism mode)

prob.class-class

Prob class union for performance metric objects

show,PMobj-method

Show the output of a PM

makeTransparent

Make colors transparent

Join Data objects present in a list

Sample Observation Parameters

Calculate TAC recommendations for more than one MP

Class 'Stock'

Sample Implementation Error Parameters

Stock class objects

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

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

Returns Results of a set of MICE relationships

Apply Management Procedures to an object of class Data

Double-normal selectivity curve

Extract the first dimension of a hierarchical list of recommendation objects

Calculate CV from vector of values

Wrapper for histogram function

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

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

show,Rec-method

Show the output of a single MP recommendation

Biomass wormplot

Internal function to write CSVs for objects

Run a Management Procedure

Runs input control MPs on a Data object.

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

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

Determine optimal number of cpus

Aging and Mortality for one time-step

Internal wrapper function to calculate MSY reference points

Population dynamics for a MICE model (single year)

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

Performance Whisker Plot

Manually map the historical relative fishing effort trajectory.

SimulatedData Data

read.projection.file

Reads iSCAM projection file

Tom's expand grid

Current default thresholds for DFO satisficing

read.report.file

Reads iSCAM Rep file

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

Generate a Data Report

Import Fleet Object from Excel file

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

Remove observation, implementation, and process error

summary,MSE-method

Summary of MSE object

Import Stock Object from Excel file

Generic Trade-Plot Function

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

Load OM from Excel file

Utility functions for MSE objects

Calculate Mean Probability

Blow parallel optimization function

Get part of an MP specific data-list

Calculate Probability

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

genSizeCompWrap

Wrapper for C++ function to generate length composition

Combines indices into a single index using linear modelling

Combines all iSCAM age composition data across fleets

Combine data among fleets

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

Combine data among stocks

label.class-class

Label class union for performance metric objects

Plot several plots with a shared legend

Dimensions of a hierarchical list object

Print out plotting functions

A generic OFL plot for NOAA use

A fairly tidy time-series quantile plot

A basic SSB plot for debugging runMSE output

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

load.iscam.files

Reads iSCAM files into a hierarchical R list object

Plot Operating Model Object

Population dynamics for a MICE model (multiyear)

Plot MSE object

Population dynamics model in CPP

Setup parallel processing

Lognormal distribution for DLMtool

Valid custom parameters (cpars)

Reads iSCAM parameter file

summary,Data-method

Summary of Data object

Reads iSCAM mcmc output files

Calculates movement matrices from user inputs