Learn R Programming

⚠️There's a newer version (6.0.7) of this package.Take me there.

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.

Copy Link

Version

Install

install.packages('DLMtool')

Monthly Downloads

352

Version

5.0.1

License

GPL-2

Maintainer

Tom Carruthers

Last Published

November 24th, 2017

Functions in DLMtool (5.0.1)

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

Beddington and Kirkwood life-history MP (simple version)

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

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

Atlantic_mackerel

Atlantic_mackerel Data

Blow internal parallel optimization function

Blue_shark Stock

Performance Metric: Probability AAVY < 0.2

Constant catch management procedure of Geromont and Butterworth (2014)

Butterfish Stock

COSEWIC forward projection plot

Constant catch management procedure of Geromont and Butterworth (2014)

Manually map the historical relative fishing effort trajectory.

Manually choose the historical selectivity pattern

Manually map natural mortality at age or size.

Bluefin_tuna Stock

Catch at size reduction analysis

MSE convergence diagnostic

China_rockfish Data

Optimization function for CSRA

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

Check Data object is valid for a MP

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

Check that a DLM object is valid

Apply input control recommendations and calculate population dynamics

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

Apply output control recommendations and calculate population dynamics

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

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

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

Bluefin_tuna_WAtl

Bluefin_tuna_WAtl Stock

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

Effort searching MP aiming for 50 per cent stock depletion

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

Depletion Adjusted Average Catch

Depletion-Based Stock Reduction Analysis

Deparment of Fisheries and Oceans historical plot

Depletion Corrected Average Catch paired with the 40-10 rule

Depletion Corrected Average Catch assuming 40 per cent stock depletion

Check Convergence

Deparment of Fisheries and Oceans trade-off plot

Plot the median biomass and yield relative to last historical year

Deparment of Fisheries and Oceans default plot 2

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

Example_datafile

Example_datafile Data

DecE_HDom Fleet

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

A reference FMSY method (uses perfect information about FMSY)

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

Load more data from DLMextra package

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

DLMtool-package

Data-Limited Methods Toolkit

Demographic FMSY method

Dynamic Fratio MP

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

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

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

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

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

An FMSY/M ratio method

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

IncE_NDom Fleet

Geromont and Butterworth index slope Harvest Control Rule

Function to run a set of input control methods

Geromont and Butterworth target CPUE and catch MP

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

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

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

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

Indian Ocean Tuna Commission trade-off plot

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

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

Class 'Fleet'

Geromont and Butterworth Constant Catch Harvest Control Rule

FleetDescription

FleetDescription

Generic_IncE Fleet

Internal optimization function for delay-difference MPs

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

Delay - Difference Stock Assessment with UMSY and MSY leading

How dominant is an MP?

Deparment of Fisheries and Oceans projection plot

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

Effort searching MP aiming for 40 per cent stock depletion

Class 'InputRec'

DataDescription

DataDescription

Mean index ratio MP from Jardim et al. 2015

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

Class 'Fease'

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

MP feasibility diagnostic

Low_Effort_Non_Target

Low_Effort_Non_Target Fleet

Feasibility2 Fease

Return class of MP from MP name

FlatE_Dom Fleet

Generic_Obs Obs

Gulf_blue_tilefish

Gulf_blue_tilefish Data

Directory of the installed package on your computer

Hybrid Depletion Adjusted Average Catch

Feasibility Fease

DecE_NDom Fleet

FlatE_HDom Fleet

Depletion Corrected Fratio

FlatE_NDom Fleet

Read in feasibility parameters from Excel spreadsheet

Generic_DecE Fleet

Read in Data object from Excel spreadsheet

Index Target 10

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

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

Data needed to get MPs running

Internal estimation function for LSRA and LSRA2 functions

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

Initialize Operating Model

Imprecise_Biased

Imprecise_Biased Obs

Length to age conversion

Precise_Biased Obs

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.

Precise_Unbiased

Precise_Unbiased Obs

Apply the Length-based SPR model to DLMtool Data Object

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

Length-based SPR model with HCR that iteratively adjusts Effort

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

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

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

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

Mean Catch Depletion

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

Generate OM Documentation Report

Read in operating model parameters from Excel spreadsheet

Copy example OM XL and OM Documentation

What methods need what data

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

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

Performance Metric: Probability F < FMSY

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

Standardize values

Sample Observation Parameters

Harvest Control Rule using prior for intrinsic rate of increase

Generic_FlatE Fleet

Generic_Fleet Fleet

SampleStockPars

Sample Stock parameters

Index Target based on natural mortality rate

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

Calculate TAC recommendations for more than one MP

Performance Metric: Probability B > 0.1 BMSY

Index Target Effort-Based 10

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

Imprecise_Unbiased

Imprecise_Unbiased Obs

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

IncE_HDom Fleet

Joint probability plot

Calculate Value Of Information

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

Calculate Value Of Information 2

Length-based SPR model with HCR that iteratively adjusts Selectivity

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

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.

Index Target Effort-Based 5

Performance Metric: Average Yield

Calculate Mean Probabilty

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

Calculate Probabilty

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

SampleFleetPars

Sample Fleet Parameters

Red_snapper Data

Sample Implementation Error Parameters

Surplus production based catch-limit modifier

Slope in surplus production MP

Stochastic SRA construction of operating models

Double-normal selectivity curve

StochasticSRAcpp

Stochastic SRA construction of operating models

Rcpp version of the Projection function for calculating Reference Yield

Test Trade-Off Plot

Reads data from iSCAM file structure into a DLMtool Data object

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

Generic Trade-off Plot

Internal SRA MCMC CPP code

Calculate alpha parameter for beta distribution from mean and standard deviation

Internal estimation function for LSRA and LSRA2 functions

What objects of this class are available

Conduct stock assessment

Fishing at current effort levels

Sample custom pars

Blow parallel optimization function

Calculate historical fishing mortality

Sensitivity analysis

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

Simulation_1 Data

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

Combines all iSCAM age composition data across fleets

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

Combines indices into a single index using linear modelling

initialize-methods

~~ Methods for Function initialize ~~

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

Is a value NA or zero.

Fishing at 75 per cent of current effort levels

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

Class 'Stock'

Print out plotting functions

StockDescription

StockDescription

Load OM from Excel file

Yet another Value of Information Plot

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

Make stochastic variables certain for only one rep

Check that MSE object includes all slots

Perfect_Info Obs

Generic comparison plot for simulation testing of Stochastic SRA method

Wrapper for histogram function

Reads MLE estimates from iSCAM file structure into an operating model

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

makeTransparent

Make colors transparent

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

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

Extracts growth parameters from a SS3 r4ss replist

Depletion and F estimation from mean length of catches

get object class

Calculate Statistics for MP Performance

load.iscam.files

Reads iSCAM files into a hierarchical R list object

Plot M-at-Age and Size

Population dynamics model in CPP

Convert a OM object to one without observation or process error

Population dynamics model for one annual time-step

No Fishing Reference MP

National Oceanographic and Atmospheric Administration default plot 1

Catch trend Surplus Production MSY MP

Performance Metric: Probability B > BMSY

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

Performance Metric: Probability B > 0.5 BMSY

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

Optimize yield for a single simulation

Optimize q for a single simulation

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

A generic OFL plot for NOAA use

Runs input control MPs on a Data object.

Run a Management Strategy Evaluation

Plot the vulnerability and retention curves

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

Plot the Stock object parameters

Target_All_Fish

Target_All_Fish Fleet

Population dynamics model

Targeting_Small_Fish

Targeting_Small_Fish Fleet

Toothfish Stock

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

Setup parallel processing

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

Update an MSE object with new slots

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

Open the DLMtool User Guide

Plot the operating model (OM) object parameters

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

Plot the Observation object parameters

Plot simulation test of Stochastic SRA method

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

Performance Whisker Plot

read.report.file

Reads iSCAM Rep file

Perfect_Imp Imp

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

Surplus Production Stock Reduction Analysis

summary,MSE-method

Summary of MSE object

Calculate density of log-normally distributed random numbers

Rcpp version of the Projection Optimizer

Boxplot of TAC recommendations

read.control.file

Reads iSCAM control file

Boxplot of MP performance from MSE object

Reads iSCAM parameter file

read.projection.file

Reads iSCAM projection file

Calculate CV from vector of values

optimize for catchability (q)

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

fetch.file.names

Reads iSCAM Data, Control and Projection files

Generate length composition of catch

label.class-class

Label class union for performance metric objects

show,PMobj-method

Show the output of a PM

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

Simulate population dynamics for historical years

Manually map the historical relative fishing effort trajectory.

Internal function to write CSVs for objects

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

Subset an OM cpars slot

Plot a barplot of MSE results

Calculate beta parameter for beta distribution from mean and standard deviation

A trade-off plot for an MSE object

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

Rcpp version of the q Optimizer

Calculate FMSY and related metrics using Rcpp code

Example data object

Calculate Reference Yield

Plot the Implementation object parameters

Calculate selectivity curve

plot,MSE,ANY-method

Plot MSE object

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

Population dynamics model for one annual time-step

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

prob.class-class

Prob class union for performance metric objects

Run a Management Strategy Evaluation

runMSE with no messages - for testing

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

Generate log-normally distributed random numbers

A function that samples multivariate normal (logspace) variables

Reads iSCAM dat file

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

Reads iSCAM mcmc output files

plot,Data,ANY-method

Plot Data object

sample_steepness2

Sample steepness given mean and cv

Valid custom parameters (cpars)

Plot the Fleet object parameters

Biomass wormplot

An data-limited method which sets a slot limit

summary,Data-method

Summary of Data object