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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 and Documentation

A DLMtool User Guide and documentation for the DLMtool package are now available: https://dlmtool.github.io/DLMtool/.

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

389

Version

5.1.3

License

GPL-2

Maintainer

Tom Carruthers

Last Published

March 26th, 2018

Functions in DLMtool (5.1.3)

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

Atlantic_mackerel

Atlantic_mackerel Data

Beddington and Kirkwood life-history method combined with catch curve analysis

Constant catch management procedure of Geromont and Butterworth (2014)

Beddington and Kirkwood life-history analysis with mean-length estimator of current abundance

Constant catch management procedure of Geromont and Butterworth (2014)

Performance Metric: Probability AAVY < 0.2

Blue_shark Stock

Catch at size reduction analysis

Beddington and Kirkwood life-history MP (simple version)

Bluefin_tuna Stock

Depletion Corrected Average Catch assuming 40 per cent stock depletion

Manually map natural mortality at age or size.

Blow internal parallel optimization function

Plot the median biomass and yield relative to last historical year

COSEWIC forward projection plot

Manually choose the historical selectivity pattern

Depletion Adjusted Average Catch

Bluefin_tuna_WAtl

Bluefin_tuna_WAtl Stock

Butterfish Stock

Deparment of Fisheries and Oceans trade-off plot

Depletion-Based Stock Reduction Analysis using mean-length estimator of current depletion

Average Catch with a size limit

Initialize an empty Data workbook or CSV

Age-composition-based estimate of current stock depletion given constant Z linked to an FMSY estimate to provide OFL

Delay - Difference Stock Assessment with UMSY and MSY leading

Optimization function for CSRA

Read in Data object from Excel spreadsheet

Age-composition-based estimate of current stock depletion given constant Z linked to an FMSY estimate to provide OFL (with a 40-10 rule)

What management procedures can be applied to this Data object?

An adaptive MP that uses trajectory in inferred suplus production and fishing mortality rate to update a TAC

Depletion Corrected Average Catch paired with the 40-10 rule

Check Convergence

Demographic FMSY method

What management procedures can't be applied to this DLM data object

Depletion-Based Stock Reduction Analysis

Check that a DLM object is valid

Effort searching MP aiming for 50 per cent stock depletion

Depletion-Based Stock Reduction Analysis paired with 40-10 harvest control rule

Delay - Difference Stock Assessment with UMSY and MSY leading coupled with a 40-10 harvest control rule

Deparment of Fisheries and Oceans default plot 2

Deparment of Fisheries and Oceans historical plot

Load more data from DLMextra package

Manually map the historical relative fishing effort trajectory.

Deparment of Fisheries and Oceans projection plot

Dynamic Fratio MP

Directory of the installed package on your computer

Effort searching MP aiming for 40 per cent stock depletion

Depletion-Based Stock Reduction Analysis assuming 40 per cent stock depletion

Effort MP: adjust effort up/down if mean length above/below Ltarget

Effort control version of DD - Delay - Difference Stock Assessment with UMSY and MSY leading that fishes at 75 per cent of FMSY

DLMtool-package

Data-Limited Methods Toolkit

Depletion Corrected Average Catch

Class 'Fease'

How dominant is an MP?

Example_datafile

Example_datafile Data

A reference FMSY method that fishes at half of FMSY (uses perfect information about FMSY)

Effort searching version of DD - Delay - Difference Stock Assessment with UMSY and MSY leading that fishes at 75 per cent of FMSY

A reference FMSY method (uses perfect information about FMSY)

MP feasibility diagnostic

Read in feasibility parameters from Excel spreadsheet

China_rockfish Data

An FMSY/M ratio method paired with the 40-10 rule

Feasibility Fease

A data-limited method that uses FMSY/M ratio and a naive catch-curve estimate of recent Z

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

Demographic FMSY method using catch-curve analysis to estimate recent Z

DataDescription

DataDescription

Generic_FlatE Fleet

An FMSY/M ratio method

Demographic FMSY method that uses mean length data to estimate recent Z

Effort control version of DD - Delay - Difference Stock Assessment with UMSY and MSY leading

Generic_Fleet Fleet

Generic_IncE Fleet

Geromont and Butterworth index slope Harvest Control Rule

Generic_Obs Obs

Imprecise_Biased

Imprecise_Biased Obs

An FMSY/M ratio MP that uses a mean length estimator of recent Z

Geromont and Butterworth target CPUE and catch MP

DecE_HDom Fleet

A example mixed control MP that uses the Itarget1 output control MP together with a spatial closure.

Geromont and Butterworth Constant Catch Harvest Control Rule

A reference FMSY method that fishes at three quarters of FMSY (uses perfect information about FMSY)

A management procedure that incrementally adjusts the TAC (starting from reference level that is a fraction of mean recent catches) to reach a target CPUE / relative abundance index

DecE_NDom Fleet

FlatE_HDom Fleet

Index Confidence Interval (ICI) MP by Jardim et al. (2015)

Index Target 10

Mean index ratio MP from Jardim et al. 2015

Index Target Effort-Based 5

FlatE_NDom Fleet

A management procedure that incrementally adjusts the TAC to maintain a constant CPUE or relative abundance index

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

IncE_NDom Fleet

A management procedure that incrementally adjusts the effort to reach a target CPUE / relative abundance index

Depletion Corrected Fratio

Length to age conversion

A management procedure that incrementally adjusts the Effort to reach a target CPUE / relative abundance index

Function to run a set of input control methods

Low_Effort_Non_Target

Low_Effort_Non_Target Fleet

Gulf_blue_tilefish

Gulf_blue_tilefish Data

Feasibility2 Fease

Index Target Effort-Based 10

Mean length-based indicator MP of Jardim et al. 2015 using Beverton-Holt invariant M/K ratio = 1.5 and assumes FMSY = M.

Hybrid Depletion Adjusted Average Catch

Mean Catch Depletion

Imprecise_Unbiased

Imprecise_Unbiased Obs

FlatE_Dom Fleet

Generic_DecE Fleet

Index Target based on natural mortality rate

Class 'Fleet'

IncE_HDom Fleet

Less Precautionary Index Confidence Interval (ICI) MP by Jardim et al. (2015)

FleetDescription

FleetDescription

A management procedure that incrementally adjusts the TAC according to the mean length of recent catches.

Indian Ocean Tuna Commission trade-off plot

A management procedure that adjusts the TAC up/down from reference (target) level (that is a fraction of mean recent premanagement catches) to reach a target mean length of fish caught.

A management procedure that incrementally adjusts the TAC according to the mean length of recent catches.

A management procedure that incrementally adjusts the TAC to maintain a constant CPUE or relative abundance index

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

Initialize Operating Model

Calculate Statistics for MP Performance

A management procedure that incrementally adjusts the Effort according to the mean length of recent catches.

Depletion and F estimation from mean length of catches

Management Procedure Type

National Oceanographic and Atmospheric Administration default plot 1

Performance Whisker Plot

A management procedure that incrementally adjusts the TAC to reach a target mean length in catches.

Data needed to get MPs running

Perfect_Imp Imp

A management procedure that incrementally adjusts the TAC (starting from reference level that is a fraction of mean recent catches) to reach a target CPUE / relative abundance index

Performance Metric: Probability B > BMSY

An marine reserve in area 1 with no spatial reallocation of fishing effort

Red_snapper Data

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

Performance Metric: Probability B > 0.5 BMSY

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

A marine reserve in area 1 with full reallocation of fishing effort

Internal SRA MCMC CPP code

A management procedure that incrementally adjusts the Effort to reach a target mean length in catches.

Internal estimation function for LSRA and LSRA2 functions

Mean Catch Depletion

Performance Metric: Probability Long-Term Yield > 0.5 Relative Yield

Performance Metric: Probability Short-Term Yield > 0.5 Relative Yield

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

Sample custom pars

Internal estimation function for LSRA and LSRA2 functions

Performance Metric: Probability F < FMSY

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

The more general version of the mean length-based indicator MP of Jardim et al. 2015.

A management procedure that incrementally adjusts the Effort to reach a target mean length in catches.

Perfect_Info Obs

Target_All_Fish

Target_All_Fish Fleet

Is a value NA or zero.

A management procedure that incrementally adjusts the TAC according to the mean length of recent catches.

No Fishing Reference MP

SampleFleetPars

Sample Fleet Parameters

MP using prior for intrinsic rate of increase with a quadratic approximation to surplus production

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

Sample Implementation Error Parameters

A management procedure that incrementally adjusts the TAC to reach a target mean length in catches.

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

Class 'Stock'

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

StockDescription

StockDescription

Load OM from Excel file

Make stochastic variables certain for only one rep

Function that returns a stochastic estimate of steepness given observed stock recruitment data

Calculate Value Of Information

Sensitivity analysis

Yield Per Recruit analysis to get FMSY proxy F01

Calculate Value Of Information 2

Precise_Biased Obs

SimulatedData Data

Surplus Production Stock Reduction Analysis

Boxplot of TAC recommendations

Precise_Unbiased

Precise_Unbiased Obs

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

Reads MLE estimates from Stock Synthesis file structure into an operating model using package r4ss

Calculate Mean Probabilty

Generate OM Documentation Report

Reads data Stock Synthesis file structure into an data object using package r4ss

Catch trend Surplus Production MSY MP

Copy example OM XL and OM Documentation

Yield Per Recruit analysis to get FMSY proxy F01 paired with a mean-length estimate of current stock size

Yet another Value of Information Plot

Calculate TAC recommendations for more than one MP

Calculate historical fishing mortality

Import a Data object from Excel file

makeTransparent

Make colors transparent

Calculate Reference Yield

A trade-off plot for an MSE object

A data-limited method in which fishing retention is set according to the maturity curve NEW

Performance Metric: Average Yield

Wrapper for histogram function

A shorter version of the plot method for MSEs that just shows the overall trade-offs

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

Reads MLE estimates from iSCAM file structure into an operating model

Calculate alpha parameter for beta distribution from mean and standard deviation

A function that samples multivariate normal (logspace) variables

Plot the Historical Spatial Closures

Yield Per Recruit analysis to get FMSY proxy F01 paired to a naive catch curve estimate of recent Z

Fishing at 75 per cent of current effort levels

Stochastic SRA construction of operating models

Population dynamics model for one annual time-step

Slope in surplus production MP

StochasticSRAcpp

Stochastic SRA construction of operating models

prob.class-class

Prob class union for performance metric objects

Calculate CV from vector of values

Plot simulation test of Stochastic SRA method

Calculate selectivity curve

Test Trade-Off Plot

Extracts growth parameters from a SS3 r4ss replist

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

Sample Observation Parameters

Performance Metric: Probability B > 0.1 BMSY

get object class

This input control sets the minimum length of fish caught to a fraction of the length that maximises the biomass, Lopt.

Simplified a multi-area transition matrix into the best 2 x 2 representation

SampleStockPars

Sample Stock parameters

Optimize q for a single simulation

Standardize values

Plot M-at-Age and Size

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

A generic OFL plot for NOAA use

Wrapper for estimating stock recruitment parameters from resampled stock-recruitment data

Harvest Control Rule using prior for intrinsic rate of increase

optimize for catchability (q)

Determine optimal number of cpus

Plot the vulnerability and retention curves

What management procedures need what data

Plot MSE object

Print out plotting functions

Optimize yield for a single simulation

runMSE with no messages - for testing

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

Biomass wormplot

Run a Management Strategy Evaluation

Runs input control MPs on a Data object.

Internal function to write CSVs for objects

sample_steepness2

Sample steepness given mean and cv

Surplus Production Stock Reduction Analysis using a mean-length estimate of current stock depletion

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

Generate log-normally distributed random numbers

Subset an OM cpars slot

Surplus production based catch-limit modifier

Generic Trade-off Plot

Double-normal selectivity curve

Apply Management Procedures to an object of class Data

Plot a barplot of MSE results

Combines indices into a single index using linear modelling

initialize-methods

~~ Methods for Function initialize ~~

What objects of this class are available

Calculate beta parameter for beta distribution from mean and standard deviation

Calculate Probabilty

Reads data from iSCAM file structure into a DLMtool Data object

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

Check that MSE object includes all slots

A data-limited method in which fishing vulnerability is set slightly higher than the maturity curve

Combines all iSCAM age composition data across fleets

load.iscam.files

Reads iSCAM files into a hierarchical R list object

derive_beta_par

This function reduces the CV by 5 per cent until steepness values can be sampled without error

Get log normal mean from transformed space mean and standard deviation

Update an MSE object with new slots

Fishing at current effort levels

summary,Data-method

Summary of Data object

Convert a OM object to one without observation or process error

Plot the Observation object parameters

fetch.file.names

Reads iSCAM Data, Control and Projection files

Example data object

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

summary,MSE-method

Summary of MSE object

Plot Data object

Plot the Fleet object parameters

Simulation_1 Data

read.report.file

Reads iSCAM Rep file

read.projection.file

Reads iSCAM projection file

read.control.file

Reads iSCAM control file

Manually map the historical relative fishing effort trajectory.

Run a Management Procedure

Targeting_Small_Fish

Targeting_Small_Fish Fleet

Reads iSCAM dat file

Predict Beverton-Holt recruitment and return fit to S-R observations

Toothfish Stock

Run a Management Strategy Evaluation

show,PMobj-method

Show the output of a PM

Blow parallel optimization function

Generic comparison plot for simulation testing of Stochastic SRA method

Join multiple MSE objects together

Calculate density of log-normally distributed random numbers

show,Rec-method

Show the output of a single MP recommendation

label.class-class

Label class union for performance metric objects

Population dynamics model in CPP

Plot the Implementation object parameters

Simulate population dynamics for historical years

Reads iSCAM mcmc output files

Plot the operating model (OM) object parameters

An data-limited method which sets a slot limit

Reads iSCAM parameter file

Setup parallel processing

Plot the Stock object parameters

Get log normal standard deviation from transformed space mean and standard deviation

Open the DLMtool User Guide

Valid custom parameters (cpars)