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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 are now 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

5.4.1

License

GPL-2

Maintainer

Tom Carruthers

Last Published

December 6th, 2019

Functions in DLMtool (5.4.1)

Geromont and Butterworth (2015) Constant Catch

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

Beddington and Kirkwood life-history MP

Catch at size reduction analysis

Average Catch with a size limit

Check the years to summarize performance

Manually map parameters for the historical period of operating model

Delay - Difference Stock Assessment

Calculate population dynamics from MP recommendation

Effort-based Delay - Difference Stock Assessment

Identify management procedures (MPs) based on data availability

Delay-Difference Internal Function

What Data objects can be used to run this MP?

Delay-Difference Internal Function

Current default thresholds for COSEWIC satificing

Check Convergence

Deparment of Fisheries and Oceans trade-off plot

Plot the median biomass and yield relative to last historical year

Age-Composition Stock-Reduction Analysis

Internal function for CompSRA MP

Check that a DLM object is valid

Depletion-Based Stock Reduction Analysis

Depletion Corrected Average Catch

DFO_tab_formatted

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

Adaptive Fratio

Initialize Data Input Files

Reference management procedures

DataDescription

DataDescription

Depletion Corrected Average Catch

Create a standard DFO performance table

Depletion-based SRA internal function

Geromont and Butterworth target CPUE and catch MP

Deparment of Fisheries and Oceans projection plot

Directory of the installed package on your computer

Fleet class objects

MP feasibility diagnostic

DLMenv blank environment

Deparment of Fisheries and Oceans biomass quantile plot

Kalman filter and Rauch-Tung-Striebel smoother

Imp class objects

Deparment of Fisheries and Oceans stock status bar plot

Class 'Fleet'

Converts a Data object into a .csv data file

Deparment of Fisheries and Oceans default plot 2

Index Target Internal Function

Deparment of Fisheries and Oceans historical plot

Load more data from DLMextra package

DLMtool-package

Data-Limited Methods Toolkit

Dynamic Fratio MP

Mean Index Ratio

Index Target Effort-Based

Read in Data object from Excel spreadsheet

Incremental Index Target MP

Geromont and Butterworth Constant Catch Harvest Control Rule

Effort Target Optimum Length

Index Slope Internal Function

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

Index Slope Tracking MP

Internal SRA MCMC CPP code

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

Geromont and Butterworth index slope Harvest Control Rule

Step-wise Constant Catch

Get help topic URL

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

Management Procedure Type

FMSY/M ratio methods

Determine dominate MPs

Iterative Index Target MP

Fratio internal function

Index Confidence Interval

Catch trend Surplus Production MSY MP

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

Surplus Production Stock Reduction Analysis

Standardize values

Function to run a set of input control methods

Index Target based on natural mortality rate

Length to age conversion

Length-Based SPR MPs

Internal optimization function

Create a standard DFO MSE report

DFO performance spider plot (top three MPs)

Internal estimation function for LSRA and LSRA2 functions

Internal estimation function for LSRA and LSRA2 functions

Calculate Statistics for MP Performance

Depletion and F estimation from mean length of catches

Initialize Operating Model

Estimate length-weight parameters from data

Internal Estimation Function for LBSPR MP

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

Internal function to calculate MSY Reference Points

Effort searching MP aiming for a fixed stock depletion

StockDescription

StockDescription

Generic Trade-off Plot

Class 'Stock'

Atlantic_mackerel

Data class objects

Manually map the historical relative fishing effort trajectory.

Stochastic SRA construction of operating models

Obs class objects

Indian Ocean Tuna Commission trade-off plot

Demographic FMSY method

Incremental Index Target MP Internal Function

PerformanceMetric

Performance Metrics Methods

What management procedures need what data

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

Class union for isRel slot

optimize for catchability (q)

Opens the DLMtool Cheat-Sheets (requires internet connection)

Boxplot of TAC recommendations

Plot a barplot of MSE results

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

Sensitivity analysis

SimulatedData Data

label.class-class

Label class union for performance metric objects

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

Internal function for Fdem MP

FleetDescription

FleetDescription

Create an MP that averages the results of multiple MPs

Forces correlation among operating model parameters for M, K, Linf and L50

Itarget1 with an MPA

Incremental Index Target MP - Effort-Based A management procedure that incrementally adjusts the fishing effort to reach a target CPUE / relative abundance index

Performance Whisker Plot

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

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

Generate a Data Report

Incremental Index Target MP Internal Function - Effort MP

Internal estimation function for LBSPR MP

Determine optimal number of cpus

Spatial closure and allocation management procedures

Length Target TAE MP

Mean Catch Depletion

Generate OM Documentation Report

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

Copy example OM XL and OM Documentation

Surplus Production Stock Reduction Analysis Internal Function

Predict missing life-history parameters

StochasticSRAcpp

Stochastic SRA construction of operating models

Step-wise Constant Effort

Run a Management Strategy Evaluation

Plot Operating Model Object

Optimize yield for a single simulation

Print out plotting functions

sample_steepness2

Sample steepness given mean and cv

Value of Information Plot using PM functions

Length Target TAC MP

Is a value NA or zero.

Surplus production based catch-limit modifier

Stock class objects

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

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

Calculate Value Of Information

Sample custom pars

Subset an OM cpars slot

Apply Management Procedures to an object of class Data

Find the Management Procedures that use a particular data slot

Import a Data object from Excel file

What objects of this class are available

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

Remove observation, implementation, and process error

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

Calculate selectivity curve

Wrapper for histogram function

Double-normal selectivity curve

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

Internal function for YPR MPs

Internal demographic function

Size limit management procedures

Internal function to estimate r

National Oceanographic and Atmospheric Administration default plot 1

Blow parallel optimization function

Create a table of Performance Limits and Performance Objectives

Intrinsic rate of Increase MP

Slope in surplus production MP

MP feasibility diagnostic using real data

Plot simulation test of Stochastic SRA method

Valid custom parameters (cpars)

Make stochastic variables certain for only one rep

Biomass wormplot

SampleFleetPars

Sample Fleet Parameters

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

Plot M-at-Age and Size

Calculate historical fishing mortality

Join Data objects present in a list

Sample Implementation Error Parameters

Yield Per Recruit analysis to get FMSY proxy F01

Yet another Value of Information Plot

Calculate TAC recommendations for more than one MP

Utility functions for MSE objects

Plot several plots with a shared legend

Calculate Value Of Information 2

Load OM from Excel file

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

Plot the Fleet object parameters

Generic comparison plot for simulation testing of Stochastic SRA method

SampleStockPars

Sample Stock parameters

Plot the Historical Spatial Closures

Sample Observation Parameters

Plot the Implementation object parameters

Current default thresholds for DFO satificing

prob.class-class

Prob class union for performance metric objects

show,PMobj-method

Show the output of a PM

Setup parallel processing

Population dynamics model for one annual time-step

Calculate Mean Probability

Generic Trade-Plot Function

Trade-off plots for an MSE object

Calculate Probability

Fishing at current effort levels

Calculate CV from vector of values

COSEWIC MSE run using the correct MPs and projected time horizon

summary,Data-method

Summary of Data object

Plot the vulnerability and retention curves

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

A generic OFL plot for NOAA use

Internal function to write CSVs for objects

Simulate Catch-at-Length Data

genSizeCompWrap

Wrapper for C++ function to generate length composition

Calculate Reference Yield

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

get object class

Population dynamics model in CPP

makeTransparent

Make colors transparent

Optimize q for a single simulation

Convert a OM object to one without observation or process error

Plot the Stock object parameters

Internal wrapper function to calculate MSY reference points

initialize-methods

~~ Methods for Function initialize ~~

Inverse von Bertalanffy

Plot the operating model (OM) object parameters

Plot the Observation object parameters

Plot Data object

Plot MSE object

Run a Management Procedure

Simulate Catch-at-Age Data

show,Rec-method

Show the output of a single MP recommendation

Runs input control MPs on a Data object.

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

summary,MSE-method

Summary of MSE object

Open the DLMtool User Guide

Lognormal distribution for DLMtool

Blow internal parallel optimization function

Optimization function for CSRA

Age-based Catch Curve

Simplifies the CAL slot of data object