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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

5.0.2

License

GPL-2

Maintainer

Tom Carruthers

Last Published

November 25th, 2017

Functions in DLMtool (5.0.2)

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

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

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

Beddington and Kirkwood life-history MP (simple version)

Blue_shark Stock

Blow internal parallel optimization function

Performance Metric: Probability AAVY < 0.2

Atlantic_mackerel

Atlantic_mackerel Data

Catch at size reduction analysis

Optimization function for CSRA

Manually choose the historical selectivity pattern

Bluefin_tuna Stock

Bluefin_tuna_WAtl

Bluefin_tuna_WAtl Stock

Constant catch management procedure of Geromont and Butterworth (2014)

MSE convergence diagnostic

China_rockfish Data

COSEWIC forward projection plot

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

Manually map the historical relative fishing effort trajectory.

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

Manually map natural mortality at age or size.

Check Convergence

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

Plot the median biomass and yield relative to last historical year

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

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

Effort searching MP aiming for 50 per cent stock depletion

Internal optimization function for delay-difference MPs

Depletion Corrected Average Catch paired with the 40-10 rule

Butterfish Stock

Depletion Corrected Average Catch assuming 40 per cent stock depletion

Constant catch management procedure of Geromont and Butterworth (2014)

What data-limited methods can be applied to this Data object?

Deparment of Fisheries and Oceans trade-off plot

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

Deparment of Fisheries and Oceans default plot 2

Delay - Difference Stock Assessment with UMSY and MSY leading

DataDescription

DataDescription

Deparment of Fisheries and Oceans projection plot

Directory of the installed package on your computer

Read in Data object from Excel spreadsheet

What methods can't be applied to this DLM data object

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

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

Depletion Corrected Average Catch

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

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

How dominant is an MP?

Example_datafile

Example_datafile Data

Effort searching MP aiming for 40 per cent stock depletion

A reference FMSY method (uses perfect information about FMSY)

DecE_HDom Fleet

Class 'Fease'

Read in feasibility parameters from Excel spreadsheet

Class 'Fleet'

MP feasibility diagnostic

FleetDescription

FleetDescription

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

Generic_DecE Fleet

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

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

Indian Ocean Tuna Commission trade-off plot

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

Class 'InputRec'

Geromont and Butterworth Constant Catch Harvest Control Rule

Feasibility Fease

Feasibility2 Fease

Gulf_blue_tilefish

Gulf_blue_tilefish Data

FlatE_Dom Fleet

Hybrid Depletion Adjusted Average Catch

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

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

Apply the Length-based SPR model to DLMtool Data Object

Imprecise_Biased

Imprecise_Biased Obs

Length-based SPR model with HCR that iteratively adjusts Effort

DecE_NDom Fleet

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

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

Depletion Corrected Fratio

Mean index ratio MP from Jardim et al. 2015

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

Joint probability plot

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

Demographic FMSY method

Length-based SPR model with HCR that iteratively adjusts Selectivity

Return class of MP from MP name

Generic_FlatE Fleet

Generic_Fleet Fleet

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

Index Target 10

Generate OM Documentation Report

Length-based SPR model with HCR that iteratively adjusts TAC

Copy example OM XL and OM Documentation

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

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

Depletion and F estimation from mean length of catches

Make stochastic variables certain for only one rep

Performance Whisker Plot

Index Target Effort-Based 5

Perfect_Imp Imp

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

An FMSY/M ratio method

Geromont and Butterworth index slope Harvest Control Rule

Apply input control recommendations and calculate population dynamics

Length to age conversion

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.

Apply output control recommendations and calculate population dynamics

Internal SRA MCMC CPP code

Internal estimation function for LSRA and LSRA2 functions

Check Data object is valid for a MP

Calculate Statistics for MP Performance

Data needed to get MPs running

Check that a DLM object is valid

Depletion Adjusted Average Catch

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

Performance Metric: Probability F < FMSY

Geromont and Butterworth target CPUE and catch MP

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

Index Target based on natural mortality rate

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

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

Index Target Effort-Based 10

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

IncE_NDom Fleet

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

Function to run a set of input control methods

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

Surplus production based catch-limit modifier

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

Slope in surplus production MP

Mean Catch Depletion

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

Manually map the historical relative fishing effort trajectory.

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

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

Mean Catch Depletion

Target_All_Fish

Target_All_Fish Fleet

Read in operating model parameters from Excel spreadsheet

A trade-off plot for an MSE object

Performance Metric: Probability B > BMSY

Performance Metric: Probability B > 0.5 BMSY

Perfect_Info Obs

Catch trend Surplus Production MSY MP

Conduct stock assessment

Scatter plot of B/BMSY or B/B0 and F/FMSY for lastYrs

Sample custom pars

Stochastic SRA construction of operating models

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

StochasticSRAcpp

Stochastic SRA construction of operating models

Yield Per Recruit analysis to get FMSY proxy F01

Targeting_Small_Fish

Targeting_Small_Fish Fleet

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

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

What methods need what data

Fishing at current effort levels

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

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

Fishing at 75 per cent of current effort levels

Sample Observation Parameters

fetch.file.names

Reads iSCAM Data, Control and Projection files

SampleStockPars

Sample Stock parameters

Depletion-Based Stock Reduction Analysis

Generate length composition of catch

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

Wrapper for histogram function

Deparment of Fisheries and Oceans historical plot

Load more data from DLMextra package

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

Toothfish Stock

DLMtool-package

Data-Limited Methods Toolkit

Boxplot of TAC recommendations

Boxplot of MP performance from MSE object

Dynamic Fratio MP

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

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

Is a value NA or zero.

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

Performance Metric: Probability B > 0.1 BMSY

Reads MLE estimates from iSCAM file structure into an operating model

Precise_Biased Obs

makeTransparent

Make colors transparent

Precise_Unbiased

Precise_Unbiased Obs

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

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

FlatE_HDom Fleet

Optimization function that returns the squared difference between user specified and calculated movement parameters. (deprecated: now in Rcpp)

FlatE_NDom Fleet

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

Generic_IncE Fleet

Generic_Obs Obs

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

Red_snapper Data

Plot simulation test of Stochastic SRA method

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

plot,Data,ANY-method

Plot Data object

Plot the Fleet object parameters

Imprecise_Unbiased

Imprecise_Unbiased Obs

Population dynamics model for one annual time-step

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

prob.class-class

Prob class union for performance metric objects

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

Sensitivity analysis

Subset an OM cpars slot

Simulation_1 Data

Yet another Value of Information Plot

Class 'Stock'

Check that MSE object includes all slots

Generic comparison plot for simulation testing of Stochastic SRA method

StockDescription

StockDescription

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

sample_steepness2

Sample steepness given mean and cv

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

IncE_HDom Fleet

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

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

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

Reads data from iSCAM file structure into a DLMtool Data object

Get log normal mean from transformed space mean and standard deviation

Optimize yield for a single simulation

Combines all iSCAM age composition data across fleets

Optimize q for a single simulation

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

Plot the Implementation object parameters

Load OM from Excel file

plot,MSE,ANY-method

Plot MSE object

Rcpp version of the Projection Optimizer

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

read.control.file

Reads iSCAM control file

Performance Metric: Average Yield

read.report.file

Reads iSCAM Rep file

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

show,PMobj-method

Show the output of a PM

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

Simulate population dynamics for historical years

Setup parallel processing

Valid custom parameters (cpars)

Calculate Value Of Information

Biomass wormplot

Internal estimation function for LSRA and LSRA2 functions

Calculate Value Of Information 2

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

Calculate alpha parameter for beta distribution from mean and standard deviation

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

What objects of this class are available

Low_Effort_Non_Target

Low_Effort_Non_Target Fleet

Calculate selectivity curve

Calculate CV from vector of values

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

derive_beta_par

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

Join multiple MSE objects together

Double-normal selectivity curve

label.class-class

Label class union for performance metric objects

Convert a OM object to one without observation or process error

Rcpp version of the Projection function for calculating Reference Yield

A function that samples multivariate normal (logspace) variables

Blow parallel optimization function

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

Calculate historical fishing mortality

A generic OFL plot for NOAA use

Plot the vulnerability and retention curves

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

Plot the Stock object parameters

optimize for catchability (q)

Population dynamics model

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

load.iscam.files

Reads iSCAM files into a hierarchical R list object

National Oceanographic and Atmospheric Administration default plot 1

No Fishing Reference MP

Initialize Operating Model

Rcpp version of the q Optimizer

Example data object

Print out plotting functions

Standardize values

Harvest Control Rule using prior for intrinsic rate of increase

Reads iSCAM parameter file

Surplus Production Stock Reduction Analysis

read.projection.file

Reads iSCAM projection file

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

An data-limited method which sets a slot limit

summary,Data-method

Summary of Data object

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

Sample Implementation Error Parameters

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

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

Calculate TAC recommendations for more than one MP

SampleFleetPars

Sample Fleet Parameters

Test Trade-Off Plot

Plot M-at-Age and Size

Generic Trade-off Plot

Plot a barplot of MSE results

Population dynamics model in CPP

Calculate beta parameter for beta distribution from mean and standard deviation

Population dynamics model for one annual time-step

Calculate Mean Probabilty

Update an MSE object with new slots

Calculate Probabilty

runMSE with no messages - for testing

Open the DLMtool User Guide

Run a Management Strategy Evaluation

Calculate FMSY and related metrics using Rcpp code

summary,MSE-method

Summary of MSE object

initialize-methods

~~ Methods for Function initialize ~~

Calculate Reference Yield

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

Extracts growth parameters from a SS3 r4ss replist

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

Plot the operating model (OM) object parameters

get object class

Calculate density of log-normally distributed random numbers

Combines indices into a single index using linear modelling

Plot the Observation object parameters

Generate log-normally distributed random numbers

Internal function to write CSVs for objects

Reads iSCAM dat file

Reads iSCAM mcmc output files

Runs input control MPs on a Data object.

Run a Management Strategy Evaluation