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DLMtool

DLMtool is a R package for management strategy evaluation and implementation of data-limited fishery stock assessment methods.

Find more information about DLMtool at http://datalimitedtoolkit.org/.

Installation

The released version of DLMtool can be downloaded from CRAN:

install.packages("DLMtool")

This GitHub repository contains the development version of DLMtool. The development version may be unstable, and it is not recommended for analyses.

User Guide

A User Guide for the DLMtool package is available: https://dlmtool.github.io/DLMtool/userguide/introduction.html.

Bugs and Issues

Please report any bugs or issues through GitHub or the DLMtool website.

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Version

Install

install.packages('DLMtool')

Monthly Downloads

594

Version

5.4.5

License

GPL-2

Maintainer

Tom Carruthers

Last Published

June 16th, 2020

Functions in DLMtool (5.4.5)

Catch at size reduction analysis

Optimization function for CSRA

Age-Composition Stock-Reduction Analysis

Plot the median biomass and yield relative to last historical year

Depletion-Based Stock Reduction Analysis

Internal function for CompSRA MP

Create a standard DFO performance table

Check Convergence

Age-based Catch Curve

Geromont and Butterworth (2015) Constant Catch

Current default thresholds for COSEWIC satificing

Depletion Corrected Average Catch

Delay - Difference Stock Assessment

DFO_tab_formatted

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

Blow internal parallel optimization function

Depletion Corrected Average Catch

Beddington and Kirkwood life-history MP

Average Catch with a size limit

Converts a Data object into a .csv data file

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

Simplifies the CAL slot of data object

Deparment of Fisheries and Oceans trade-off plot

Check that a DLM object is valid

Depletion-based SRA internal function

What Data objects can be used to run this MP?

Calculate population dynamics from MP recommendation

Manually map parameters for the historical period of operating model

Dynamic Fratio MP

Check the years to summarize performance

Delay-Difference Internal Function

Effort Target Optimum Length

Effort-based Delay - Difference Stock Assessment

Deparment of Fisheries and Oceans default plot 2

Create a standard DFO MSE report

Deparment of Fisheries and Oceans projection plot

Delay-Difference Internal Function

Deparment of Fisheries and Oceans stock status bar plot

Deparment of Fisheries and Oceans historical plot

Deparment of Fisheries and Oceans biomass quantile plot

Identify management procedures (MPs) based on data availability

Internal optimization function

DFO performance spider plot (top three MPs)

DataDescription

DataDescription

Load more data from DLMextra package

Directory of the installed package on your computer

Demographic FMSY method

FleetDescription

FleetDescription

MP feasibility diagnostic

DLMenv blank environment

Internal function for Fdem MP

DLMtool-package

Data-Limited Methods Toolkit

FMSY/M ratio methods

Read in Data object from Excel spreadsheet

Determine dominate MPs

Geromont and Butterworth Constant Catch Harvest Control Rule

Kalman filter and Rauch-Tung-Striebel smoother

Indian Ocean Tuna Commission trade-off plot

Initialize Data Input Files

Generate bootstrapped estimates of von Bertalanffy growth parameters from length-at-age data

Fratio internal function

Geromont and Butterworth target CPUE and catch MP

Geromont and Butterworth index slope Harvest Control Rule

Index Target based on natural mortality rate

Effort searching MP aiming for a fixed stock depletion

Reference management procedures

Atlantic_mackerel

Data class objects

Function to run a set of input control methods

Incremental Index Target MP Internal Function - Effort MP

Index Confidence Interval

Incremental Index Target MP - Effort-Based

Adaptive Fratio

Incremental Index Target MP Internal Function

Incremental Index Target MP

Index Target Internal Function

Iterative Index Target MP

Predict missing life-history parameters

Itarget1 with an MPA

Estimate length-weight parameters from data

Mean Index Ratio

Internal estimation function for LSRA and LSRA2 functions

Length to age conversion

Estimates R0 using SRA to match current F estimates and avoid penalities for low stock sizes

Alternative version of LSRA that's a wrapper for LSRA_opt to return the right type of output (mode) using sapply

Length Target TAC MP

Internal SRA MCMC CPP code

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

Generate a Data Report

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

Length-Based SPR MPs

Step-wise Constant Catch

Index Target Effort-Based

Fleet class objects

Class 'Fleet'

Calculate Statistics for MP Performance

Management Procedure Type

Mean length-based indicator MP of Jardim et al. 2015

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

Step-wise Constant Effort

Plot simulation test of Stochastic SRA method

Mean Catch Depletion

Internal estimation function for LSRA and LSRA2 functions

Copy example OM XL and OM Documentation

National Oceanographic and Atmospheric Administration default plot 1

Length Target TAE MP

Simulates catch at age and catch history data for testing SRA methods

Internal function to calculate MSY Reference Points

Is a value NA or zero.

Make stochastic variables certain for only one rep

Initialize Operating Model

Depletion and F estimation from mean length of catches

Imp class objects

Stochastic SRA construction of operating models

StochasticSRAcpp

Stochastic SRA construction of operating models

Index Slope Internal Function

Index Slope Tracking MP

Internal Estimation Function for LBSPR MP

Create a table of Performance Limits and Performance Objectives

Obs class objects

Get help topic URL

Internal estimation function for LBSPR MP

Spatial closure and allocation management procedures

Surplus Production Stock Reduction Analysis

Generate OM Documentation Report

Manually map the historical relative fishing effort trajectory.

Performance Whisker Plot

Stock class objects

SimulatedData Data

Surplus Production Stock Reduction Analysis Internal Function

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

PerformanceMetric

Performance Metrics Methods

Trade-off plots for an MSE object

Value of Information Plot using PM functions

Yet another Value of Information Plot

MP feasibility diagnostic using real data

Boxplot of TAC recommendations

Current default thresholds for DFO satificing

Calculate Mean Probability

Class 'Stock'

Sample custom pars

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

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

Generic Trade-Plot Function

SampleFleetPars

Sample Fleet Parameters

Generic comparison plot for simulation testing of Stochastic SRA method

Plot Data object

Create an MP that averages the results of multiple MPs

Convert a OM object to one without observation or process error

Plot the Observation object parameters

What objects of this class are available

Generic Trade-off Plot

Plot a barplot of MSE results

Standardize values

Intrinsic rate of Increase MP

Catch trend Surplus Production MSY MP

Slope in surplus production MP

Yield Per Recruit analysis to get FMSY proxy F01

Surplus production based catch-limit modifier

Fishing at current effort levels

Internal function of runMSE for checking that the OM slot cpars slot is formatted correctly

Calculate selectivity curve

Internal function for YPR MPs

StockDescription

StockDescription

What management procedures need what data

makeTransparent

Make colors transparent

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

Wrapper for histogram function

Calculate CV from vector of values

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

Blow parallel optimization function

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

Size limit management procedures

Inverse von Bertalanffy

Sample Implementation Error Parameters

Internal demographic function

Find the Management Procedures that use a particular data slot

Calculate Value Of Information

Subset an OM cpars slot

Sample Observation Parameters

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

Plot the Implementation object parameters

Plot the Fleet object parameters

SampleStockPars

Sample Stock parameters

optimize for catchability (q)

Internal function to estimate r

Plot several plots with a shared legend

Plot MSE object

Optimize q for a single simulation

Plot Operating Model Object

Print out plotting functions

Sensitivity analysis

label.class-class

Label class union for performance metric objects

A generic OFL plot for NOAA use

Plot the Historical Spatial Closures

show,PMobj-method

Show the output of a PM

Plot the operating model (OM) object parameters

Plot the vulnerability and retention curves

Calculate TAC recommendations for more than one MP

Import a Data object from Excel file

COSEWIC MSE run using the correct MPs and projected time horizon

show,Rec-method

Show the output of a single MP recommendation

Load OM from Excel file

Double-normal selectivity curve

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

Apply Management Procedures to an object of class Data

Plot M-at-Age and Size

Calculate Value Of Information 2

sample_steepness2

Sample steepness given mean and cv

Plot the Stock object parameters

Utility functions for MSE objects

Opens the DLMtool Cheat-Sheets (requires internet connection)

Calculate Reference Yield

Join Data objects present in a list

Calculate historical fishing mortality

initialize-methods

~~ Methods for Function initialize ~~

Open the DLMtool User Guide

get object class

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.

Optimize yield for a single simulation

Valid custom parameters (cpars)

Run a Management Procedure

Calculate Probability

Class union for isRel slot

Internal wrapper function to calculate MSY reference points

genSizeCompWrap

Wrapper for C++ function to generate length composition

Run a Management Strategy Evaluation

summary,MSE-method

Summary of MSE object

prob.class-class

Prob class union for performance metric objects

summary,Data-method

Summary of Data object

Biomass wormplot

Determine optimal number of cpus

Internal function to write CSVs for objects

Population dynamics model in CPP

Population dynamics model for one annual time-step

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

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

Setup parallel processing

Simulate Catch-at-Age Data

Simulate Catch-at-Length Data

Runs input control MPs on a Data object.

Remove observation, implementation, and process error

Lognormal distribution for DLMtool