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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

4.4.1

License

GPL-2

Maintainer

Tom Carruthers

Last Published

August 3rd, 2017

Functions in DLMtool (4.4.1)

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

Blow internal parallel optimization function

Beddington and Kirkwood life-history MP (simple version)

Blue_shark Stock

Bluefin_tuna Stock

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

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

Atlantic_mackerel

Atlantic_mackerel Data

Constant catch management procedure of Geromont and Butterworth (2014)

Constant catch management procedure of Geromont and Butterworth (2014)

Manually map natural mortality at age or size.

Optimization function for CSRA

Apply input control recommendations and calculate population dynamics

Check that a DLM object is valid

Manually map the historical relative fishing effort trajectory.

Depletion-Based Stock Reduction Analysis

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

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

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

Apply output control recommendations and calculate population dynamics

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

Bluefin_tuna_WAtl

Bluefin_tuna_WAtl Stock

Butterfish Stock

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

MSE convergence diagnostic

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)

COSEWIC forward projection plot

Catch at size reduction analysis

China_rockfish Data

Check Data object is valid for a MP

Manually choose the historical selectivity pattern

Plot the median biomass and yield relative to last historical year

Depletion Adjusted Average Catch

Delay - Difference Stock Assessment with UMSY and MSY leading

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

How dominant is an MP?

Effort searching MP aiming for 40 per cent stock depletion

Internal function FMSY and related metrics

Feasibility2 Fease

FlatE_Dom Fleet

Class 'Fleet'

A reference FMSY method (uses perfect information about FMSY)

Read in feasibility parameters from Excel spreadsheet

Feasibility Fease

An FMSY/M ratio method

Depletion Corrected Average Catch

Depletion Corrected Average Catch paired with the 40-10 rule

Depletion Corrected Average Catch assuming 40 per cent stock depletion

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

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

Generic_DecE Fleet

Generic_FlatE Fleet

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

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

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

Internal optimization function for delay-difference MPs

Index Target based on natural mortality rate

Index Target Effort-Based 10

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 (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 Effort to reach a target CPUE / relative abundance index

Joint probability plot

Internal estimation function for LSRA and LSRA2 functions

Deparment of Fisheries and Oceans projection plot

DecE_HDom Fleet

DecE_NDom Fleet

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

Effort searching MP aiming for 50 per cent stock depletion

Depletion Corrected Fratio

Deparment of Fisheries and Oceans default plot 2

Dynamic Fratio MP

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

Demographic FMSY method

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

Internal estimation function for LSRA and LSRA2 functions

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.

Depletion and F estimation from mean length of catches

Calculate Statistics for MP Performance

Read in operating model parameters from Excel spreadsheet

Red_snapper Data

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

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

Geromont and Butterworth target CPUE and catch MP

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

Catch trend Surplus Production MSY MP

Surplus Production Stock Reduction Analysis

Selectivity at length function

Sensitivity analysis

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

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

FlatE_HDom Fleet

FlatE_NDom Fleet

Generic_obs Obs

Load more data from DLMdata package

Index Target Effort-Based 5

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

Gulf_blue_tilefish

Gulf_blue_tilefish Data

Hybrid Depletion Adjusted Average Catch

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

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

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.

Stochastic SRA construction of operating models

Stochastic SRA construction of operating models

Calculate TAC recommendations for more than one MP

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

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

Check Convergence

Deparment of Fisheries and Oceans historical plot

Deparment of Fisheries and Oceans trade-off plot

Calculate alpha parameter for beta distribution from mean and standard deviation

Calculate beta parameter for beta distribution from mean and standard deviation

Boxplot of TAC recommendations

Rcpp version of the Projection function for calculating Reference Yield

Indian Ocean Tuna Commission trade-off plot

Imprecise_Biased

Imprecise_Biased Obs

Imprecise_Unbiased

Imprecise_Unbiased Obs

Directory of the installed package on your computer

DLMtool-package

Data-Limited Methods Toolkit

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

Example_datafile

Example_datafile Data

Class 'Fease'

MP feasibility diagnostic

Geromont and Butterworth Constant Catch Harvest Control Rule

Geromont and Butterworth index slope Harvest Control Rule

Function to run a set of input control methods

Class 'InputRec'

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 effort to reach a target CPUE / relative abundance index

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

Low_Effort_Non_Target

Low_Effort_Non_Target Fleet

Length-based SPR model with HCR that iteratively adjusts Effort

Length-based SPR model with HCR that iteratively adjusts Selectivity

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.

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.

No Fishing Reference MP

National Oceanographic and Atmospheric Administration default plot 1

Generic_IncE Fleet

Generic_fleet Fleet

Index Target 10

Data needed to get MPs running

What methods need what data

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.

Return class of MP from MP name

fetch.file.names

Reads iSCAM Data, Control and Projection files

Calculate FMSY and related metrics using Rcpp code

Calculate FMSY and related metrics using Rcpp code

Wrapper for histogram function

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

Surplus production based catch-limit modifier

Reads MLE estimates from iSCAM file structure into an operating model

Convert a OM object to one without observation or process error

makeTransparent

Make colors transparent

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

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

Print out plotting functions

Plot M-at-Age and Size

Population dynamics model for one annual time-step

SampleFleetPars

Sample Fleet Parameters

Rcpp version of the Projection Optimizer

read.report.file

Reads iSCAM Rep file

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

sample_steepness2

Sample steepness given mean and cv

Apply the Length-based SPR model to DLMtool Data Object

Length-based SPR model with HCR that iteratively adjusts TAC

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

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

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

Perfect_Imp Imp

Perfect_Info Obs

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

Precise_Biased Obs

Sample Implementation Error Parameters

Class 'Stock'

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

Target_All_Fish

Target_All_Fish Fleet

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

Is a value NA or zero.

Targeting_Small_Fish

Targeting_Small_Fish Fleet

Calculate Value Of Information 2

Yet another Value of Information Plot

Generic comparison plot for simulation testing of Stochastic SRA method

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

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

Conduct stock assessment

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

Blow parallel optimization function

Internal Get Reference F

Internal Get Reference F using Rcpp

Calculate slope from ageM and age95

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

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

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

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

Internal function to optimize for F

Rcpp version of the q Optimizer

Example data object

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

Precise_Unbiased

Precise_Unbiased Obs

Standardize values

Slope in surplus production MP

Plot simulation test of Stochastic SRA method

Sample Observation Parameters

SampleStockPars

Sample Stock parameters

SetRecruitCycle

Function to calculate cyclic recruitment pattern given user-specified values of period and amplitude.

Sample custom pars

Manually map the historical relative fishing effort trajectory.

Subset an OM cpars slot

IncE_HDom Fleet

IncE_NDom Fleet

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

Length to age conversion

Population dynamics model in CPP

Population dynamics model for one annual time-step

Reads iSCAM parameter file

read.projection.file

Reads iSCAM projection file

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

Internal SRA MCMC CPP code

Mean Catch Depletion

Mean Catch Depletion

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

Make stochastic variables certain for only one rep

Simulation_1 Data

Toothfish Stock

A trade-off plot for an MSE object

What objects of this class are available

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

Setup parallel processing

Open the DLMtool User Guide

Valid custom parameters (cpars)

Harvest Control Rule using prior for intrinsic rate of increase

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

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

Internal Two sided selectivity curve

Calculate Value Of Information

Fishing at 75 per cent of current effort levels

Plot a barplot of MSE results

Boxplot of MP performance from MSE object

Check that MSE object includes all slots

derive_beta_par

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

Calculate CV from vector of values

Calculate historical fishing mortality

Internal function to calculate slope

Internal Projection Function

Calculate Reference Yield

Internal function to calculate F-at-age given catch and biomass

Optimization function that find the catchability (q where F=qE) value required to get to user-specified stock depletion (current biomass / unfished biomass) modified for Rcpp

optimize for catchability (q)

Reads data from iSCAM file structure into a DLMtool Data object

Combines all iSCAM age composition data across fleets

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

Calculate FMSY and related metrics

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

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

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

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

Generic Trade-off Plot

Yield Per Recruit analysis to get FMSY proxy F01

A function that samples multivariate normal (logspace) variables

Plot the Implementation object parameters

plot,MSE,ANY-method

Plot MSE object

Plot the Stock object parameters

Population dynamics model

Reads iSCAM dat file

Reads iSCAM mcmc output files

Simulate population dynamics for historical years

An data-limited method which sets a slot limit

Internal function to calculate slope

get object class

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

Combines indices into a single index using linear modelling

Generate log-normally distributed random numbers

Update an MSE object with new slots

initialize-methods

~~ Methods for Function initialize ~~

Optimize yield for a single simulation

Optimize q for a single simulation

plot,Data,ANY-method

Plot Data object

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

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

Fishing at current effort levels

Plot the Fleet object parameters

Internal optimization function that find the catchability (q where F=qE) value required to get to user-specified stock depletion (current biomass / unfished biomass)

read.control.file

Reads iSCAM control file

runMSE with no messages - for testing

Run a Management Strategy Evaluation

summary,Data-method

Summary of Data object

summary,MSE-method

Summary of MSE object

Generate length composition of catch

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

Extracts growth parameters from a SS3 r4ss replist

Internal function to calculate ascending slope of selectivity curve

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

Optimization function that find the catchability (q where F=qE) value required to get to user-specified stock depletion (current biomass / unfished biomass)

Join multiple MSE objects together

load.iscam.files

Reads iSCAM files into a hierarchical R list object

Get log normal mean from transformed space mean and standard deviation

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

Plot the operating model (OM) object parameters

Plot the Observation object parameters

A generic OFL plot for NOAA use

Plot the vulnerability and retention curves

Runs input control MPs on a Data object.

Run a Management Strategy Evaluation

Calculate density of log-normally distributed random numbers

Biomass wormplot

Internal function to write CSVs for objects