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DLMtool (version 3.1)

Data-Limited Methods Toolkit

Description

Simulation testing and implementation of data-limited fishery stock assessment methods.

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Version

Install

install.packages('DLMtool')

Monthly Downloads

389

Version

3.1

License

GPL-2

Maintainer

Tom Carruthers

Last Published

February 27th, 2016

Functions in DLMtool (3.1)

PorgMSE

Example MSE object used in the vignette
DepF

Depletion Corrected Fratio
IT5

Index Target 5
CheckConverg

MSE convergence diagnostic
DynF

Dynamic Fratio MP
FMSYref75

A reference FMSY method that fishes at three quarters of FMSY (uses perfect information about FMSY)
Islope4

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

Index Target based on natural mortality rate
PMs

Built-in Performance metrics
FMSYref

A reference FMSY method (uses perfect information about FMSY)
Itarget4

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.
DBSRA

Depletion-Based Stock Reduction Analysis
ChooseEffort

Manually choose the historical relative fishing effort trajectory.
DD4010

Delay - Difference Stock Assessment with UMSY and MSY leading coupled with a 40-10 harvest control rule
DBSRA4010

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

Data-Limited Methods Toolkit
MRreal

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

Extra Depletion Corrected Average Catch
Ltarget1

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

Catch at size reduction analysis
DoOpt

Optimization routine for LBSPR methods
NOAA_plot

National Oceanographic and Atmospheric Administration default plot 1
DLM_general-class

Class "DLM_general"
Pplot

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

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

What data-limited methods can be applied to this DLM_data object?
NAor0

Is a value NA or zero.
DLM_data-class

Class "DLM_data"
Fdem_CC

Demographic FMSY method using catch-curve analysis to estimate recent Z
DCAC_40

Depletion Corrected Average Catch assuming 40 per cent stock depletion
Needed

Data needed to get MPs running
Fleet-class

Class "Fleet"
GB_CC

Geromont and Butterworth Constant Catch Harvest Control Rule
Rcontrol2

MP using prior for intrinsic rate of increase with a quadratic approximation to surplus production
DBSRA_40

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

Example MSE object used in the vignette
Fratio

An FMSY/M ratio method
CompSRA

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

Mean Catch Depletion
Ltarget4

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

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

Class "Observation"
GB_slope

Geromont and Butterworth index slope Harvest Control Rule
SBT1

SBT simple MP
L2A

Length to age conversion
Fratio4010

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

Slope in surplus production MP
CC4

Constant catch management procedure of Geromont and Butterworth (2014)
LBSPRSim

Per-Recruit Length-Based Spawning Potential Ratio Simulation Model
LBSPR_ItEff

Length-based SPR model with HCR that iteratively adjusts Effort
OM-class

Class "OM"
matlenlim

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

Optimization function for CSRA
IT10

Index Target 10
Kplot

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

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

Kalman filter and Rauch-Tung-Striebel smoother
Sam

Conduct stock assessment
SPmod

Surplus production based catch-limit modifier
plotOFL

A generic OFL plot for NOAA use
GB_target

Geromont and Butterworth target CPUE and catch MP
DLM_fease-class

Class "DLM_fease"
DCAC

Depletion Corrected Average Catch
DLMDataDir

Directory of the installed package on your computer
DLMdat

Data and Operating model objects
DD

Delay - Difference Stock Assessment with UMSY and MSY leading
BK_CC

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

Comparison plots for individual simulations
MRnoreal

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

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

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

Calculate Value Of Information
CompSRA4010

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

Apply LBSPR model to time-series of catch-at-length
SBT2

SBT complex MP
Fdem_ML

Demographic FMSY method that uses mean length data to estimate recent Z
FMSYref50

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

A trade-off plot for an MSE object
initialize-methods

~~ Methods for Function initialize ~~
Sense

Sensitivity analysis
Fdem

Demographic FMSY method
AvC

An MP where the TAC is average historical catch
BK_ML

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

How dominant is an MP?
LBSPR_ItTAC

Length-based SPR model with HCR that iteratively adjusts TAC
Itarget1

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.
DBSRA_ML

Depletion-Based Stock Reduction Analysis using mean length estimator of stock depletion
matlenlim2

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

What methods need what data
Fratio_CC

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

G-control MP
getAFC

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

Fishing at current effort levels
LstepCC1

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

Length-based SPR model with HCR that iteratively adjusts Selectivity.
runMSE

Run a Management Strategy Evaluation
MCD4010

Mean Catch Depletion
MSE-class

Class "MSE"
Tplot2

A trade-off plot for an MSE object that compares long-term yield (LTY: fraction of simulations getting over half FMSY yield in the last ten years of the projection), short-term yield (STY: fraction of simulations getting over half FMSY yield in the first ten years of the projection), variability in yield (VY: fraction of simulations where average annual variability in yield is less than 10 per cent) and biomass level (B10: the fraction of simulations in which biomass stays above 10 percent of BMSY).
Rcontrol

Harvest Control Rule using prior for intrinsic rate of increase
qopt

Internal optimization function that find the catchability (q where F=qE) value required to get to user-specified stock depletion (current biomass / unfished biomass)
Islope1

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

Surplus Production Stock Reduction Analysis
avail

What objects of this class are available
SPMSY

Catch trend Surplus Production MSY MP
TradePlot

Generic Trade-off Plot
YPR_ML

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

Calculate TAC recommendations for more than one MP
OptFun

Objective function for LBSPR methods
getq

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

Example data object
ourMSE

Example MSE object used in the vignette
summary-methods

~~ Methods for Function summary ~~
runInMP

Runs input control MPs on a DLM_data object.
curE75

Fishing at 75 per cent of current effort levels
YPR_CC

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

Class "Stock"
replic8

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

~~ Methods for Function plot ~~
YPR

Yield Per Recruit analysis to get FMSY proxy F01
getmov

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

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

Optimization function that returns the squared difference between user specified and calculated movement parameters.
ML2D

Depletion and F estimation from mean length of catches
CC1

Constant catch management procedure of Geromont and Butterworth (2014)
LstepCC4

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

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

Beddington and Kirkwood life-history MP (simple version)
DCAC4010

Depletion Corrected Average Catch paired with the 40-10 rule
Fease

MP feasibility diagnostic
lmmodel-class

Class "lmmodel"