Learn R Programming

⚠️There's a newer version (6.0.6) 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

389

Version

4.1

License

GPL-2

Maintainer

Tom Carruthers

Last Published

May 2nd, 2017

Functions in DLMtool (4.1)

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

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

Blow internal parallel optimization function

Arrowtooth_Flounder_BC_DFO_iSCAM

Arrowtooth_Flounder_BC_DFO_iSCAM OM

Atlantic_mackerel

Atlantic_mackerel Data

Beddington and Kirkwood life-history MP (simple version)

COSEWIC forward projection plot

Catch at size reduction analysis

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

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

Constant catch management procedure of Geromont and Butterworth (2014)

Constant catch management procedure of Geromont and Butterworth (2014)

Canary_Rockfish_BC_DFO

Canary_Rockfish_BC_DFO OM

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

Blue_shark Stock

Bluefin_tuna Stock

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

Manually map the historical relative fishing effort trajectory.

Manually choose the historical selectivity pattern

Depletion Corrected Average Catch assuming 40 per cent stock depletion

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

Bluefin_tuna_WAtl

Bluefin_tuna_WAtl Stock

Butterfish Stock

MSE convergence diagnostic

China_rockfish Data

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

Read in feasibility parameters from Excel spreadsheet

Feasibility Fease

Optimization function for CSRA

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

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

Depletion Corrected Average Catch

Effort searching MP aiming for 50 per cent stock depletion

Darnley_Bay_Char_DFO

Darnley_Bay_Char_DFO OM

Internal function FMSY and related metrics

A reference FMSY method (uses perfect information about FMSY)

Class 'Fleet'

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

Generic_IncE Fleet

Generic_fleet Fleet

Plot the median biomass and yield relative to last historical year

Depletion Adjusted 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 default plot 2

Deparment of Fisheries and Oceans projection plot

Depletion Corrected Fratio

Dynamic Fratio MP

Imprecise_Biased

Imprecise_Biased Obs

Imprecise_Unbiased

Imprecise_Unbiased Obs

Joint probability plot

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

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

Demographic FMSY method

An FMSY/M ratio method

Generic_DecE Fleet

Generic_FlatE Fleet

Index Target based on natural mortality rate

Index Target Effort-Based 10

Index Target Effort-Based 5

How dominant is an MP?

Effort searching MP aiming for 40 per cent stock depletion

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

Example_datafile

Example_datafile Data

Depletion Corrected Average Catch paired with the 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

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

Internal estimation function for LSRA and LSRA2 functions

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.

No Fishing Reference MP

National Oceanographic and Atmospheric Administration default plot 1

Red_snapper_GOM_SS

Red_snapper_GOM_SS OM

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)

Feasibility2 Fease

FlatE_Dom Fleet

Class 'Fease'

MP feasibility diagnostic

Geromont and Butterworth target CPUE and catch MP

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

Generic_obs Obs

Gulf_blue_tilefish

Gulf_blue_tilefish Data

Hybrid Depletion Adjusted Average Catch

Depletion-Based Stock Reduction Analysis

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

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

Index Target 10

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

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

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

Mean Catch Depletion

Directory of the installed package on your computer

IncE_NDom Fleet

Function to run a set of input control methods

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.

Is a value NA or zero.

Read in operating model parameters from Excel spreadsheet

Apply the Length-based SPR model to DLMtool Data Object

Length-based SPR model with HCR that iteratively adjusts Effort

Length-based SPR model with HCR that iteratively adjusts Selectivity

Data needed to get MPs running

Catch trend Surplus Production MSY MP

Conduct stock assessment

San_Francisco_Bay_herring_California

San_Francisco_Bay_herring_California OM

Manually map the historical relative fishing effort trajectory.

Calculate Value Of Information

Calculate Value Of Information 2

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 TAC (starting from reference level that is a fraction of mean recent catches) to reach a target CPUE / relative abundance index

DLMtool-package

Data-Limited Methods Toolkit

DecE_HDom Fleet

DecE_NDom Fleet

Check that MSE object includes all slots

Generic comparison plot for simulation testing of Stochastic SRA method

Internal Get Reference F using Rcpp

Extracts growth parameters from a SS3 r4ss replist

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 Effort according to the mean length of recent catches.

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

Low_Effort_Non_Target

Low_Effort_Non_Target Fleet

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 TAC according to the mean length of recent catches.

load.iscam.files

Reads iSCAM files into a hierarchical R list object

Convert a OM object to one without observation or process error

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

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

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

Precise_Biased Obs

Calculate Statistics for MP Performance

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

Make stochastic variables certain for only one rep

Perfect_Imp Imp

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

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

Rougheye_Rockfish_BC

Rougheye_Rockfish_BC OM

Rcpp version of the q Optimizer

Example data object

read.report.file

Reads iSCAM Rep file

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

Standardize values

Surplus production based catch-limit modifier

Slope in surplus production MP

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

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

Surplus Production Stock Reduction Analysis

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

SetRecruitCycle

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

Simulation_1 Data

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

Precise_Unbiased

Precise_Unbiased Obs

Red_Snapper_GOM

Red_Snapper_GOM OM

Red_snapper Data

summary,MSE-method

Summary of MSE object

Calculate density of log-normally distributed random numbers

Selectivity at length function

Sensitivity analysis

Swordfish_OM OM

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

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

Generate length composition of catch

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

Calculate TAC recommendations for more than one MP

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

Yellowfin_Tuna_IO

Yellowfin_Tuna_IO OM

Yellowfin_tuna_IO_SS

Yellowfin_tuna_IO_SS OM

Plot simulation test of Stochastic SRA method

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

Stochastic SRA construction of operating models

A trade-off plot for an MSE object

Calculate slope from ageM and age95

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

Plot the Implementation object parameters

plot,MSE,ANY-method

Plot MSE object

Class 'Stock'

Target_All_Fish

Target_All_Fish Fleet

Yet another Value of Information Plot

A generic OFL plot for NOAA use

Rcpp version of the Projection Optimizer

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

Setup parallel processing

Generate log-normally distributed random numbers

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

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

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

Geromont and Butterworth Constant Catch Harvest Control Rule

Geromont and Butterworth index slope Harvest Control Rule

IncE_HDom Fleet

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

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

Blow parallel optimization function

Calculate FMSY and related metrics using Rcpp code

Internal Get Reference F

Generic Trade-off Plot

Internal Two sided selectivity curve

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

A function that samples multivariate normal (logspace) variables

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

Reads iSCAM parameter file

read.projection.file

Reads iSCAM projection file

Runs input control MPs on a Data object.

Run a Management Strategy Evaluation

Yield Per Recruit analysis to get FMSY proxy F01

Fishing at current effort levels

Fishing at 75 per cent of current effort levels

Calculate CV from vector of values

Boxplot of TAC recommendations

Boxplot of MP performance from MSE object

Calculate historical fishing mortality

Calculate FMSY and related metrics

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

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

Join multiple MSE objects together

Class 'lmmodel'

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.

Plot the Stock object parameters

Print out plotting functions

Internal Projection Function

Internal function to calculate slope

get object class

makeTransparent

Make colors transparent

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

Mean Catch Depletion

Depletion and F estimation from mean length of catches

Perfect_Info Obs

What methods need what data

An data-limited method which sets a slot limit

summary,Data-method

Summary of Data object

Targeting_Small_Fish

Targeting_Small_Fish Fleet

Toothfish Stock

Calculate alpha parameter for beta distribution from mean and standard deviation

What objects of this class are available

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

Plot the operating model (OM) object parameters

Plot the Observation object parameters

Reads iSCAM dat file

Reads iSCAM mcmc output files

Internal function to write CSVs for objects

Plot a barplot of MSE results

Calculate beta parameter for beta distribution from mean and standard deviation

Rcpp version of the Projection function for calculating Reference Yield

fetch.file.names

Reads iSCAM Data, Control and Projection files

Internal function to calculate ascending slope of selectivity curve

Internal function to calculate slope

Reads MLE estimates from iSCAM file structure into an operating model

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.

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

plot,Data,ANY-method

Plot Data object

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

Update an MSE object with new slots

Biomass wormplot

Run a Management Strategy Evaluation