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DLMtool

DLMtool is a R package for management strategy evalaution 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

5.2

License

GPL-2

Maintainer

Tom Carruthers

Last Published

July 10th, 2018

Functions in DLMtool (5.2)

Beddington and Kirkwood life-history MP

Age-Composition Stock-Reduction Analysis

Geromont and Butterworth (2015) Constant Catch

Current default thresholds for COSEWIC satificing

Effort-based Delay - Difference Stock Assessment

Catch at size reduction analysis

Internal function for CompSRA MP

Delay-Difference Internal Function

Average Catch with a size limit

Create a standard DFO MSE report

Depletion Corrected Average Catch

Directory of the installed package on your computer

DFO performance spider plot (top three MPs)

DLMenv blank environment

Check the years to summarize performance

Manually map parameters for the historical period of operating model

How dominant is an MP?

Load more data from DLMextra package

Deparment of Fisheries and Oceans projection plot

Deparment of Fisheries and Oceans biomass quantile plot

Blow internal parallel optimization function

Effort searching MP aiming for a fixed stock depletion

Read in Data object from Excel spreadsheet

DLMtool-package

Data-Limited Methods Toolkit

Internal optimization function

Depletion-based SRA internal function

Age-based Catch Curve

DataDescription

DataDescription

Dynamic Fratio MP

Plot the median biomass and yield relative to last historical year

Depletion-Based Stock Reduction Analysis

Initialize an empty Data workbook or CSV

Kalman filter and Rauch-Tung-Striebel smoother

Deparment of Fisheries and Oceans stock status bar plot

Internal function for Fdem MP

Fleet class objects

MP feasibility diagnostic

Geromont and Butterworth target CPUE and catch MP

Geromont and Butterworth index slope Harvest Control Rule

Deparment of Fisheries and Oceans historical plot

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

Indian Ocean Tuna Commission trade-off plot

What Data objects can be used to run this MP?

Iterative Index Target MP

Incremental Index Target MP

Check that a DLM object is valid

Deparment of Fisheries and Oceans trade-off plot

Delay - Difference Stock Assessment

Length-Based SPR Effort Control

Itarget1 with an MPA

Delay-Difference Internal Function

Spatial closure and allocation management procedures

Predict missing life-history parameters

Length to age conversion

Class 'Fleet'

Create a standard DFO performance table

Deparment of Fisheries and Oceans default plot 2

Atlantic_mackerel

Data class objects

DFO_tab_formatted

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

FleetDescription

FleetDescription

Index Target Effort-Based

Is a value NA or zero.

National Oceanographic and Atmospheric Administration default plot 1

Adaptive Fratio

Step-wise Constant Catch

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

Internal Estimation Function for LBSPR MP

Internal estimation function for LBSPR MP

Imp class objects

Performance Whisker Plot

Demographic FMSY method

FMSY/M ratio methods

Geromont and Butterworth Constant Catch Harvest Control Rule

Index Target based on natural mortality rate

Internal SRA MCMC CPP code

Fratio internal function

Internal estimation function for LSRA and LSRA2 functions

Effort Target Optimum Length

Reference management procedures

Index Target Internal Function

Index Slope Tracking MP

Generate OM Documentation Report

PerformanceMetric

Performance Metrics Methods

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

Copy example OM XL and OM Documentation

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

Index Slope Internal Function

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

Depletion and F estimation from mean length of catches

Incremental Index Target MP Internal Function - Effort MP

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

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

Calculate Statistics for MP Performance

Step-wise Constant Effort

Sample Implementation Error Parameters

Internal estimation function for LSRA and LSRA2 functions

Index Confidence Interval

Function to run a set of input control methods

Mean Index Ratio

Sample Observation Parameters

Length Target TAC MP

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

Management Procedure Type

Catch trend Surplus Production MSY MP

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

SampleStockPars

Sample Stock parameters

Incremental Index Target MP Internal Function

Sensitivity analysis

Length Target TAE MP

Get help topic URL

Stock class objects

Current default thresholds for DFO satificing

Initialize Operating Model

Mean Catch Depletion

Make stochastic variables certain for only one rep

Trade-off plots for an MSE object

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

Obs class objects

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

Surplus Production Stock Reduction Analysis

Generic Trade-Plot Function

Class 'Stock'

Generic Trade-off Plot

Plot simulation test of Stochastic SRA method

Surplus production based catch-limit modifier

Calculate Value Of Information

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

Apply Management Procedures to an object of class Data

What objects of this class are available

SampleFleetPars

Sample Fleet Parameters

Surplus Production Stock Reduction Analysis Internal Function

Value of Information Plot using PM functions

Sample custom pars

Calculate TAC recommendations for more than one MP

Calculate historical fishing mortality

Import a Data object from Excel file

Load OM from Excel file

Fishing at current effort levels

Generic comparison plot for simulation testing of Stochastic SRA method

Calculate CV from vector of values

Standardize values

Wrapper for histogram function

Calculate Reference Yield

Yield Per Recruit analysis to get FMSY proxy F01

Plot a barplot of MSE results

Utility functions for MSE objects

Intrinsic rate of Increase MP

Boxplot of TAC recommendations

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

Internal function to estimate r

Plot the operating model (OM) object parameters

get object class

optimize for catchability (q)

Slope in surplus production MP

Plot the Observation object parameters

Plot the vulnerability and retention curves

Internal demographic function

Inverse von Bertalanffy

makeTransparent

Make colors transparent

Double-normal selectivity curve

Stochastic SRA construction of operating models

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

Plot the Stock object parameters

Plot several plots with a shared legend

StochasticSRAcpp

Stochastic SRA construction of operating models

Determine optimal number of cpus

label.class-class

Label class union for performance metric objects

StockDescription

StockDescription

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

Size limit management procedures

Simulate population dynamics for historical years

summary,Data-method

Summary of Data object

Plot Data object

Run a Management Procedure

Plot the Fleet object parameters

Run a Management Strategy Evaluation

Internal function to write CSVs for objects

Plot MSE object

What management procedures need what data

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

Calculate Value Of Information 2

COSEWIC MSE run using the correct MPs and projected time horizon

Plot the Implementation object parameters

Setup parallel processing

Runs input control MPs on a Data object.

SimulatedData Data

Yet another Value of Information Plot

Manually map the historical relative fishing effort trajectory.

Calculate Mean Probability

Calculate Probability

Remove observation, implementation, and process error

Subset an OM cpars slot

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

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

prob.class-class

Prob class union for performance metric objects

Internal function for YPR MPs

sample_steepness2

Sample steepness given mean and cv

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

Calculate selectivity curve

Create an MP that averages the results of multiple MPs

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

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

Blow parallel optimization function

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

initialize-methods

~~ Methods for Function initialize ~~

Convert a OM object to one without observation or process error

Join Data objects present in a list

Lognormal distribution for DLMtool

Print out plotting functions

Open the DLMtool User Guide

Optimize yield for a single simulation

Plot M-at-Age and Size

Optimize q for a single simulation

Population dynamics model in CPP

Plot the Historical Spatial Closures

A generic OFL plot for NOAA use

Population dynamics model for one annual time-step

show,PMobj-method

Show the output of a PM

show,Rec-method

Show the output of a single MP recommendation

summary,MSE-method

Summary of MSE object

Valid custom parameters (cpars)

Biomass wormplot

Identify management procedures (MPs) based on data availability

Optimization function for CSRA

Check Convergence

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

Depletion Corrected Average Catch