Learn R Programming

⚠️There's a newer version (6.0.6) of this package.Take me there.

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.

Copy Link

Version

Install

install.packages('DLMtool')

Monthly Downloads

389

Version

5.3.1

License

GPL-2

Maintainer

Tom Carruthers

Last Published

April 29th, 2019

Functions in DLMtool (5.3.1)

Catch at size reduction analysis

Internal function for CompSRA MP

Depletion Corrected Average Catch

Depletion Corrected Average Catch

Deparment of Fisheries and Oceans projection plot

Deparment of Fisheries and Oceans biomass quantile plot

Atlantic_mackerel

Data class objects

Age-based Catch Curve

Geromont and Butterworth (2015) Constant Catch

Average Catch with a size limit

What Data objects can be used to run this MP?

Check that a DLM object is valid

Check the years to summarize performance

Plot the median biomass and yield relative to last historical year

Depletion-Based Stock Reduction Analysis

Manually map parameters for the historical period of operating model

Create a standard DFO MSE report

Delay-Difference Internal Function

DFO performance spider plot (top three MPs)

Blow internal parallel optimization function

Simplifies the CAL slot of data object

Effort-based Delay - Difference Stock Assessment

Directory of the installed package on your computer

DLMenv blank environment

Create a standard DFO performance table

Demographic FMSY method

Reference management procedures

Calculate population dynamics from MP recommendation

Identify management procedures (MPs) based on data availability

Internal function for Fdem MP

DFO_tab_formatted

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

Initialize an empty Data workbook or CSV

Read in Data object from Excel spreadsheet

Geromont and Butterworth Constant Catch Harvest Control Rule

Adaptive Fratio

Depletion-based SRA internal function

Converts a Data object into a .csv data file

DataDescription

DataDescription

FMSY/M ratio methods

Internal optimization function

Geromont and Butterworth index slope Harvest Control Rule

Index Target Effort-Based

Length-Based SPR MPs

Index Target Internal Function

National Oceanographic and Atmospheric Administration default plot 1

Is a value NA or zero.

Internal Estimation Function for LBSPR MP

Dynamic Fratio MP

Iterative Index Target MP

Deparment of Fisheries and Oceans stock status bar plot

Deparment of Fisheries and Oceans historical plot

MP feasibility diagnostic

Load more data from DLMextra package

DLMtool-package

Data-Limited Methods Toolkit

Kalman filter and Rauch-Tung-Striebel smoother

Index Target based on natural mortality rate

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

Fleet class objects

Effort Target Optimum Length

Manually map the historical relative fishing effort trajectory.

Incremental Index Target MP Internal Function

SimulatedData Data

StockDescription

StockDescription

FleetDescription

FleetDescription

Class 'Fleet'

Fratio internal function

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

Incremental Index Target MP Internal Function - Effort MP

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

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

Index Slope Tracking MP

Mean Index Ratio

Calculate Value Of Information

Length to age conversion

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

Imp class objects

Calculate Value Of Information 2

Index Slope Internal Function

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

Apply Management Procedures to an object of class Data

Beddington and Kirkwood life-history MP

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

Fishing at current effort levels

Incremental Index Target MP

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

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

Check Convergence

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

optimize for catchability (q)

Internal SRA MCMC CPP code

Function to run a set of input control methods

Current default thresholds for COSEWIC satificing

Delay - Difference Stock Assessment

Deparment of Fisheries and Oceans trade-off plot

Delay-Difference Internal Function

Estimate length-weight parameters from data

Step-wise Constant Effort

Internal function to estimate r

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

Create an MP that averages the results of multiple MPs

Step-wise Constant Catch

Internal estimation function for LBSPR MP

Calculate Statistics for MP Performance

Depletion and F estimation from mean length of catches

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

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

Management Procedure Type

Deparment of Fisheries and Oceans default plot 2

Performance Whisker Plot

How dominant is an MP?

Effort searching MP aiming for a fixed stock depletion

Geromont and Butterworth target CPUE and catch MP

Get help topic URL

Convert a OM object to one without observation or process error

Plot the Observation object parameters

Make stochastic variables certain for only one rep

Create a table of Performance Limits and Performance Objectives

Length Target TAC MP

Predict missing life-history parameters

Length Target TAE MP

Intrinsic rate of Increase MP

MP feasibility diagnostic using real data

Catch trend Surplus Production MSY MP

Mean Catch Depletion

Plot Data object

Stochastic SRA construction of operating models

Plot M-at-Age and Size

Plot simulation test of Stochastic SRA method

Initialize Operating Model

Subset an OM cpars slot

StochasticSRAcpp

Stochastic SRA construction of operating models

Internal function to calculate MSY Reference Points

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

Spatial closure and allocation management procedures

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

Plot the Historical Spatial Closures

Runs input control MPs on a Data object.

Obs class objects

Index Confidence Interval

Surplus production based catch-limit modifier

Slope in surplus production MP

Indian Ocean Tuna Commission trade-off plot

Sample Implementation Error Parameters

SampleStockPars

Sample Stock parameters

Generic Trade-Plot Function

Sensitivity analysis

Run a Management Procedure

Generic Trade-off Plot

Current default thresholds for DFO satificing

Boxplot of TAC recommendations

Calculate Mean Probability

Yet another Value of Information Plot

Trade-off plots for an MSE object

Double-normal selectivity curve

Sample Observation Parameters

Value of Information Plot using PM functions

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

Calculate TAC recommendations for more than one MP

Internal estimation function for LSRA and LSRA2 functions

What objects of this class are available

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

Plot a barplot of MSE results

Internal estimation function for LSRA and LSRA2 functions

Blow parallel optimization function

Generic comparison plot for simulation testing of Stochastic SRA method

makeTransparent

Make colors transparent

Calculate historical fishing mortality

Generate OM Documentation Report

Size limit management procedures

Plot the Implementation object parameters

Copy example OM XL and OM Documentation

Plot the operating model (OM) object parameters

genSizeCompWrap

Wrapper for C++ function to generate length composition

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

Plot MSE object

PerformanceMetric

Performance Metrics Methods

get object class

Standardize values

Print out plotting functions

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

Surplus Production Stock Reduction Analysis

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

Calculate Reference Yield

Surplus Production Stock Reduction Analysis Internal Function

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

Plot several plots with a shared legend

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

label.class-class

Label class union for performance metric objects

show,Rec-method

Show the output of a single MP recommendation

Simulate Catch-at-Age Data

Optimize yield for a single simulation

Internal wrapper function to calculate MSY reference points

Population dynamics model for one annual time-step

prob.class-class

Prob class union for performance metric objects

What management procedures need what data

Valid custom parameters (cpars)

Run a Management Strategy Evaluation

Sample custom pars

sample_steepness2

Sample steepness given mean and cv

Determine optimal number of cpus

Remove observation, implementation, and process error

SampleFleetPars

Sample Fleet Parameters

Import a Data object from Excel file

Stock class objects

Plot the Stock object parameters

Load OM from Excel file

Population dynamics model in CPP

Class 'Stock'

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

COSEWIC MSE run using the correct MPs and projected time horizon

Biomass wormplot

Calculate Probability

Class union for isRel slot

summary,MSE-method

Summary of MSE object

Opens the DLMtool Cheat-Sheets (requires internet connection)

Find the Management Procedures that use a particular data slot

Utility functions for MSE objects

Calculate selectivity curve

Yield Per Recruit analysis to get FMSY proxy F01

Internal function for YPR MPs

Calculate CV from vector of values

Internal demographic function

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

Wrapper for histogram function

Inverse von Bertalanffy

Optimize q for a single simulation

initialize-methods

~~ Methods for Function initialize ~~

Plot the Fleet object parameters

Join Data objects present in a list

A generic OFL plot for NOAA use

Plot the vulnerability and retention curves

Simulate Catch-at-Length Data

summary,Data-method

Summary of Data object

Setup parallel processing

Internal function to write CSVs for objects

show,PMobj-method

Show the output of a PM

Lognormal distribution for DLMtool

Open the DLMtool User Guide

Optimization function for CSRA

Age-Composition Stock-Reduction Analysis