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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

License

GPL-2

Maintainer

Tom Carruthers

Last Published

October 24th, 2017

Functions in DLMtool (5.0)

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

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

Catch at size reduction analysis

Optimization function for CSRA

Check Data object is valid for a MP

Check that a DLM object is valid

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

Depletion Corrected Average Catch

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

Deparment of Fisheries and Oceans historical plot

Deparment of Fisheries and Oceans trade-off plot

Deparment of Fisheries and Oceans default plot 2

DecE_HDom Fleet

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

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

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

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

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

Geromont and Butterworth Constant Catch Harvest Control Rule

Index Target based on natural mortality rate

Index Target Effort-Based 10

Imprecise_Unbiased

Imprecise_Unbiased Obs

IncE_HDom Fleet

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

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

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

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

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

Return class of MP from MP name

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

Beddington and Kirkwood life-history MP (simple version)

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

Data needed to get MPs running

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

Performance Metric: Probability F < FMSY

Performance Whisker Plot

Perfect_Imp Imp

Catch trend Surplus Production MSY MP

Constant catch management procedure of Geromont and Butterworth (2014)

COSEWIC forward projection plot

MSE convergence diagnostic

China_rockfish Data

Check Convergence

Plot the median biomass and yield relative to last historical year

Depletion Corrected Average Catch paired with the 40-10 rule

Depletion Corrected Average Catch assuming 40 per cent stock depletion

Load more data from DLMextra package

DLMtool-package

Data-Limited Methods Toolkit

DecE_NDom Fleet

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

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

Target_All_Fish

Target_All_Fish Fleet

Targeting_Small_Fish

Targeting_Small_Fish Fleet

Toothfish Stock

Plot a barplot of MSE results

Calculate beta parameter for beta distribution from mean and standard deviation

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

fetch.file.names

Reads iSCAM Data, Control and Projection files

Depletion Corrected Fratio

Read in feasibility parameters from Excel spreadsheet

Feasibility Fease

Generate length composition of catch

Extracts growth parameters from a SS3 r4ss replist

get object class

makeTransparent

Make colors transparent

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

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

FlatE_HDom Fleet

FlatE_NDom Fleet

Generic_IncE Fleet

Generic_Obs Obs

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

Index Target Effort-Based 5

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.

Internal SRA MCMC CPP code

Internal estimation function for LSRA and LSRA2 functions

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.

Mean Catch Depletion

Mean Catch Depletion

Generate OM Documentation Report

Copy example OM XL and OM Documentation

Performance Metric: Probability B > 0.1 BMSY

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

A generic OFL plot for NOAA use

Plot the vulnerability and retention curves

Population dynamics model in CPP

Population dynamics model for one annual time-step

read.report.file

Reads iSCAM Rep file

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

summary,MSE-method

Summary of MSE object

Calculate density of log-normally distributed random numbers

Update an MSE object with new slots

Open the DLMtool User Guide

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

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

Red_snapper Data

Conduct stock assessment

Sample custom pars

Manually map the historical relative fishing effort trajectory.

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

Subset an OM cpars slot

Test Trade-Off Plot

Generic Trade-off Plot

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

Performance Metric: Average Yield

Check that MSE object includes all slots

Generic comparison plot for simulation testing of Stochastic SRA method

Blow parallel optimization function

Calculate historical fishing mortality

Wrapper for histogram function

Reads MLE estimates from iSCAM file structure into an operating model

Combines indices into a single index using linear modelling

initialize-methods

~~ Methods for Function initialize ~~

A function that samples multivariate normal (logspace) variables

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

plot,Data,ANY-method

Plot Data object

Plot the Fleet object parameters

Rcpp version of the Projection Optimizer

read.control.file

Reads iSCAM control file

Runs input control MPs on a Data object.

Run a Management Strategy Evaluation

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

Setup parallel processing

Valid custom parameters (cpars)

Biomass wormplot

Performance Metric: Probability AAVY < 0.2

Butterfish Stock

Constant catch management procedure of Geromont and Butterworth (2014)

Manually map the historical relative fishing effort trajectory.

Manually map natural mortality at age or size.

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

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

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?

Effort searching MP aiming for 40 per cent stock depletion

Dynamic Fratio MP

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

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

Demographic FMSY method

Feasibility2 Fease

FlatE_Dom Fleet

Generic_FlatE Fleet

Generic_Fleet Fleet

Index Target 10

IncE_NDom Fleet

Function to run a set of input control methods

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

Length-based SPR model with HCR that iteratively adjusts Effort

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

Atlantic_mackerel

Atlantic_mackerel Data

Bluefin_tuna Stock

Blow internal parallel optimization function

Bluefin_tuna_WAtl

Bluefin_tuna_WAtl Stock

Manually choose the historical selectivity pattern

Depletion Adjusted Average Catch

Depletion-Based Stock Reduction Analysis

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

Deparment of Fisheries and Oceans projection plot

Directory of the installed package on your computer

Example_datafile

Example_datafile Data

A reference FMSY method (uses perfect information about FMSY)

Class 'Fease'

MP feasibility diagnostic

Delay - Difference Stock Assessment with UMSY and MSY leading

Blue_shark Stock

Apply input control recommendations and calculate population dynamics

Apply output control recommendations and calculate population dynamics

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

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

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

Class 'Fleet'

FleetDescription

FleetDescription

Generic_DecE Fleet

Gulf_blue_tilefish

Gulf_blue_tilefish Data

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

Internal optimization function for delay-difference MPs

Effort searching MP aiming for 50 per cent stock depletion

DataDescription

DataDescription

Hybrid Depletion Adjusted Average Catch

Class 'InputRec'

Mean index ratio MP from Jardim et al. 2015

Low_Effort_Non_Target

Low_Effort_Non_Target Fleet

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

Read in operating model parameters from Excel spreadsheet

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

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

Internal estimation function for LSRA and LSRA2 functions

Read in Data object from Excel spreadsheet

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

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

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

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

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

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

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

No Fishing Reference MP

Performance Metric: Probability B > BMSY

Performance Metric: Probability B > 0.5 BMSY

Precise_Biased Obs

Precise_Unbiased

Precise_Unbiased Obs

Surplus Production Stock Reduction Analysis

National Oceanographic and Atmospheric Administration default plot 1

Make stochastic variables certain for only one rep

Standardize values

Harvest Control Rule using prior for intrinsic rate of increase

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

What methods need what data

Surplus production based catch-limit modifier

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

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

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

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

Geromont and Butterworth index slope Harvest Control Rule

Geromont and Butterworth target CPUE and catch MP

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

Indian Ocean Tuna Commission trade-off plot

Imprecise_Biased

Imprecise_Biased Obs

Slope in surplus production MP

SampleFleetPars

Sample Fleet Parameters

Sample Implementation Error Parameters

An FMSY/M ratio method

Class 'Stock'

StockDescription

StockDescription

A trade-off plot for an MSE object

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

Yield Per Recruit analysis to get FMSY proxy F01

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

Calculate Mean Probabilty

Calculate Probabilty

Joint probability plot

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

Length-based SPR model with HCR that iteratively adjusts Selectivity

Length-based SPR model with HCR that iteratively adjusts TAC

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

Sample Observation Parameters

SampleStockPars

Sample Stock parameters

Stochastic SRA construction of operating models

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

Calculate Statistics for MP Performance

Is a value NA or zero.

Initialize Operating Model

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

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

Reads data from iSCAM file structure into a DLMtool Data object

Stochastic SRA construction of operating models

Calculate Value Of Information

Calculate Value Of Information 2

Calculate alpha parameter for beta distribution from mean and standard deviation

What objects of this class are available

Fishing at current effort levels

Fishing at 75 per cent of current effort levels

Double-normal selectivity curve

Rcpp version of the Projection function for calculating Reference Yield

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

optimize for catchability (q)

Perfect_Info Obs

Plot simulation test of Stochastic SRA method

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

Sensitivity analysis

label.class-class

Label class union for performance metric objects

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

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

Print out plotting functions

Plot M-at-Age and Size

Reads iSCAM dat file

Join multiple MSE objects together

Combines all iSCAM age composition data across fleets

load.iscam.files

Reads iSCAM files into a hierarchical R list object

Convert a OM object to one without observation or process error

Optimize yield for a single simulation

Optimize q for a single simulation

Simulation_1 Data

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

Calculate TAC recommendations for more than one MP

Plot the operating model (OM) object parameters

Plot the Observation object parameters

Plot the Stock object parameters

Yet another Value of Information Plot

Load OM from Excel file

Boxplot of TAC recommendations

Boxplot of MP performance from MSE object

Calculate CV from vector of values

Reads iSCAM mcmc output files

runMSE with no messages - for testing

Run a Management Strategy Evaluation

An data-limited method which sets a slot limit

derive_beta_par

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

Calculate FMSY and related metrics using Rcpp code

Calculate Reference Yield

Calculate selectivity curve

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

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

Get log normal mean from transformed space mean and standard deviation

summary,Data-method

Summary of Data object

Rcpp version of the q Optimizer

Example data object

Plot the Implementation object parameters

Population dynamics model

sample_steepness2

Sample steepness given mean and cv

Generate log-normally distributed random numbers

plot,MSE,ANY-method

Plot MSE object

Population dynamics model for one annual time-step

prob.class-class

Prob class union for performance metric objects

Reads iSCAM parameter file

read.projection.file

Reads iSCAM projection file

Internal function to write CSVs for objects

show,PMobj-method

Show the output of a PM

Simulate population dynamics for historical years