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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

3.2.3

License

GPL-2

Maintainer

Tom Carruthers

Last Published

April 10th, 2017

Functions in DLMtool (3.2.3)

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

Blue_shark Stock

Bluefin_tuna Stock

Bluefin_tuna_WAtl

Bluefin_tuna_WAtl Stock

Beddington and Kirkwood life-history method combined with catch curve

Atlantic_mackerel

Atlantic_mackerel DLM_data

Beddington and Kirkwood life-history MP (simple version)

Constant catch management procedure of Geromont and Butterworth (2014)

Catch at size reduction analysis

Optimization function for CSRA

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

Manually choose the historical selectivity pattern

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

Butterfish Stock

Constant catch management procedure of Geromont and Butterworth (2014)

Depletion Adjusted Average Catch

China_rockfish DLM_data

Manually map the historical relative fishing effort trajectory.

Check Convergence

Plot the median biomass and yield relative to last historical year

Delay - Difference Stock Assessment with UMSY and MSY leading coupled with a

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

DLM_fease-class

Depletion-Based Stock Reduction Analysis

Depletion-Based Stock Reduction Analysis using mean length estimator of

Depletion Corrected Average Catch

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

MSE convergence diagnostic

Age-composition-based estimate of current stock depletion given constant Z

Age-composition-based estimate of current stock depletion given constant Z

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

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

Depletion-Based Stock Reduction Analysis assuming 40 per cent stock

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

How dominant is an MP?

Effort searching MP aiming for 40 per cent stock depletion

Internal function FMSY and related metrics

A reference FMSY method (uses perfect information about FMSY)

FlatE_Dom Fleet

DLMtool-package

Data-Limited Methods Toolkit

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

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

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

Delay - Difference Stock Assessment with UMSY and MSY leading

DecE_HDom Fleet

DecE_NDom Fleet

FlatE_NDom Fleet

Effort searching version of DD - Delay - Difference Stock Assessment with

Effort searching MP aiming for 50 per cent stock depletion

Depletion Corrected Fratio

Dynamic Fratio MP

MP feasibility diagnostic

Read in feasibility parameters from Excel spreadsheet

Generic_DecE Fleet

Generic_FlatE Fleet

FlatE_HDom Fleet

An FMSY/M ratio method

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

Directory of the installed package on your computer

An adaptive MP that uses trajectory in inferred suplus production and

Demographic FMSY method

Geromont and Butterworth Constant Catch Harvest Control Rule

Geromont and Butterworth index slope Harvest Control Rule

Index Target based on natural mortality rate

Hybrid Depletion Adjusted Average Catch

Index Target Effort-Based 5

Imprecise_Biased

Imprecise_Biased Observation

Index Target 10

A management procedure that incrementally adjusts the TAC (starting from

A management procedure that incrementally adjusts the effort to reach a

A management procedure that incrementally adjusts the TAC according to the

Depletion Corrected Average Catch paired with the 40-10 rule

Depletion Corrected Average Catch assuming 40 per cent stock depletion

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

Example_datafile

Example_datafile DLM_data

Feasibility DLM_fease

Feasibility2 DLM_fease

Generic_obs Observation

Gulf_blue_tilefish

Gulf_blue_tilefish DLM_data

Imprecise_Unbiased

Imprecise_Unbiased Observation

Index Target Effort-Based 10

IncE_HDom Fleet

IncE_NDom Fleet

Length-based SPR model with HCR that iteratively adjusts Effort

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

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

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

Length-based SPR model with HCR that iteratively adjusts Selectivity

Length-based SPR model with HCR that iteratively adjusts TAC

Low_Effort_Non_Target

Low_Effort_Non_Target Fleet

Mean Catch Depletion

Function to run a set of input control methods

A management procedure that incrementally adjusts the TAC to maintain a

A management procedure that incrementally adjusts the TAC to reach a target

A management procedure that incrementally adjusts the TAC to reach a target

Mean Catch Depletion

Perfect_Info Observation

What methods need what data

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

Length to age conversion

Geromont and Butterworth target CPUE and catch MP

Generic_IncE Fleet

Generic_fleet Fleet

A management procedure that incrementally adjusts the TAC to maintain a

Depletion and F estimation from mean length of catches

Calculate Statistics for MP Performance

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

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

A management procedure that incrementally adjusts the Effort to reach a

Joint probability plot

A management procedure that incrementally adjusts the Effort to reach a

Slope in surplus production MP

A management procedure that incrementally adjusts the Effort to reach a

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

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

National Oceanographic and Atmospheric Administration default plot 1

Data needed to get MPs running

Precise_Biased Observation

Precise_Unbiased

Precise_Unbiased Observation

Selectivity at length function

Sensitivity analysis

Targeting_Small_Fish

Targeting_Small_Fish Fleet

Toothfish Stock

A management procedure that incrementally adjusts the TAC (starting from

A management procedure that adjusts the TAC up/down from reference (target)

Apply the Length-based SPR model to DLMtool Data Object

A management procedure that incrementally adjusts the TAC according to the

Standardize values

Harvest Control Rule using prior for intrinsic rate of increase

Target_All_Fish

Target_All_Fish Fleet

A trade-off plot for an MSE object

Fishing at current effort levels

Generate length composition of catch

Conduct stock assessment

Manually map the historical relative fishing effort trajectory.

A management procedure that incrementally adjusts the Effort according to

Observation-class

Make stochastic variables certain for only one rep

SetRecruitCycle

Function to calculate cyclic recruitment pattern given user-specified values

Simulation_1 DLM_data

Yield Per Recruit analysis to get FMSY proxy F01

Yield Per Recruit analysis to get FMSY proxy F01 paired to a naive catch

Calculate beta parameter for beta distribution from mean and standard deviation

boxplot.DLM_data

Boxplot of TAC recommendations

Internal Projection Function

Rcpp version of the Projection function for calculating Reference Yield

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

An data-limited method which sets a slot limit

summary,DLM_data-method

Summary of DLM_data object

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

Internal function to calculate slope

Internal function to calculate slope

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

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

Generic Trade-off Plot

Boxplot of MP performance from MSE object

A management procedure that incrementally adjusts the TAC according to the

Is a value NA or zero.

No Fishing Reference MP

Calculate Value Of Information 2

Yet another Value of Information Plot

Yield Per Recruit analysis to get FMSY proxy F01 paired with a mean-length

Calculate alpha parameter for beta distribution from mean and standard deviation

Catch trend Surplus Production MSY MP

Surplus Production Stock Reduction Analysis

Calculate TAC recommendations for more than one MP

Internal Two sided selectivity curve

Convert a OM object to one without observation or process error

makeTransparent

Make colors transparent

Example data object

plot,DLM_data-method

Plot DLM_data object

Calculate Value Of Information

What objects of this class are available

Plot a barplot of MSE results

Fishing at 75 per cent of current effort levels

Calculate CV from vector of values

Optimization function to find a movement model that matches user specified

Optimization function that find the catchability (q where F=qE) value

Optimization function that returns the squared difference between user

Rcpp version of the Optimization function that returns the squared difference between user

summary,MSE-method

Summary of MSE object

Calculate density of log-normally distributed random numbers

Read in operating model parameters from Excel spreadsheet

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

Run a Management Strategy Evaluation

Generate log-normally distributed random numbers

Update an MSE object with new slots

Check that MSE object includes all slots

Internal Get Reference F using Rcpp

Internal function to calculate ascending slope of selectivity curve

Biomass wormplot

Internal function to write CSVs for objects

Calculate historical fishing mortality

Calculate FMSY and related metrics

get object class

Red_snapper DLM_data

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

Surplus production based catch-limit modifier

Join multiple MSE objects together

A generic OFL plot for NOAA use

Rcpp version of the Projection Optimizer

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

Calculate FMSY and related metrics using Rcpp code

Internal Get Reference F

Optimization function that find the catchability (q where F=qE) value

Optimization function to find a movement model that matches user specified

A data-limited method in which fishing vulnerability is set according to the

A data-limited method in which fishing vulnerability is set slightly higher

mypars DLM_general

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

Setup parallel processing

Calculate slope from ageM and age95

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

initialize-methods

~~ Methods for Function

plot,MSE-method

Plot MSE object

Print out plotting functions

Runs input control MPs on a DLM_data object.

Run a Management Strategy Evaluation

Rcpp version of the q Optimizer

Internal optimization function that find the catchability (q where F=qE)

Enlarge (replicate) a DLM data object to create an additional dimension for