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DLMtool (version 3.2)

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

3.2

License

GPL-2

Maintainer

Tom Carruthers

Last Published

June 9th, 2016

Functions in DLMtool (3.2)

CC4

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

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

An MP where the TAC is average historical catch
CC1

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

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

What objects of this class are available
Cant

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

MSE convergence diagnostic
Can

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

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

Depletion Adjusted Average Catch
CompSRA

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

Manually choose the historical relative fishing effort trajectory.
CSRAfunc

Optimization function for CSRA
curE75

Fishing at 75 per cent of current effort levels
curE

Fishing at current effort levels
comp

Comparison plots for individual simulations
DBSRA_40

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

Catch at size reduction analysis
DBSRA4010

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

Depletion-Based Stock Reduction Analysis
DCAC_ML

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

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

Depletion Corrected Average Catch
DD

Delay - Difference Stock Assessment with UMSY and MSY leading
DCAC_40

Depletion Corrected Average Catch assuming 40 per cent stock depletion
DDe

Effort control version of DD - Delay - Difference Stock Assessment with UMSY and MSY leading
DD4010

Delay - Difference Stock Assessment with UMSY and MSY leading coupled with a 40-10 harvest control rule
DCAC4010

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

Effort searching version of DD - Delay - Difference Stock Assessment with UMSY and MSY leading that fishes at 75 per cent of FMSY
DDe75

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

Data and Operating model objects
DLMDataDir

Directory of the installed package on your computer
DLMtool-package

Data-Limited Methods Toolkit
DOM

How dominant is an MP?
DLM_fease-class

Class "DLM_fease"
DepF

Depletion Corrected Fratio
DLM_general-class

Class "DLM_general"
DLM_data-class

Class "DLM_data"
DoOpt

Optimization routine for LBSPR methods
Fdem_ML

Demographic FMSY method that uses mean length data to estimate recent Z
DTe40

Effort searching MP aiming for 40 per cent stock depletion.
Fdem

Demographic FMSY method
Fease_xl

Read in feasibility parameters from Excel spreadsheet
DTe50

Effort searching MP aiming for 50 per cent stock depletion.
Fease

MP feasibility diagnostic
DynF

Dynamic Fratio MP
Fadapt

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

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

Geromont and Butterworth index slope Harvest Control Rule
GB_CC

Geromont and Butterworth Constant Catch Harvest Control Rule
GB_target

Geromont and Butterworth target CPUE and catch MP
Gcontrol

G-control MP
Fleet-class

Class "Fleet"
getAFC

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

A reference FMSY method (uses perfect information about FMSY)
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.
getmov

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

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

Index Target based on natural mortality rate
matlenlim2

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

Join multiple MSE objects together
LBSPR_ItEff

Length-based SPR model with HCR that iteratively adjusts Effort
L2A

Length to age conversion
Ltarget4

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

An marine reserve in area 1 with no spatial reallocation of fishing effort
LtargetE1

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

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

National Oceanographic and Atmospheric Administration default plot 1
OM_xl

Read in operating model parameters from Excel spreadsheet
OM-class

Class "OM"
Sense

Sensitivity analysis
SetRecruitCycle

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

Calculate Value Of Information
YPR

Yield Per Recruit analysis to get FMSY proxy F01
VOI2

Calculate Value Of Information 2
Observation-class

Class "Observation"
Pplot

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

Surplus Production Stock Reduction Analysis
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"
YPR_ML

Yield Per Recruit analysis to get FMSY proxy F01 paired with a mean-length estimate of current stock size
Fratio4010

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

An FMSY/M ratio method
LBSPR_ItSel

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

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

Mean Catch Depletion
runMSErobust

Run a Management Strategy Evaluation
MCD4010

Mean Catch Depletion
Sam

Conduct stock assessment
SPslope

Slope in surplus production MP
HDAAC

Hybrid Depletion Adjusted Average Catch
getq

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

Surplus Production Stock Reduction Analysis using a mean-length estimate of current stock depletion
ItargetE1

A management procedure that incrementally adjusts the effort to reach a target CPUE / relative abundance index.
ItargetE4

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

Kalman filter and Rauch-Tung-Striebel smoother
LstepCE2

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

KOBE plot: a projection by projection plot of F/FMSY and B/BMSY
Ltarget1

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

Data needed to get MPs running
Sub

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

No Fishing Reference MP
VOIplot

Yet another Value of Information Plot
summary-methods

~~ Methods for Function summary ~~
plotOFL

A generic OFL plot for NOAA use
VPA

Robust Virtual Population Analysis
PorgMSE

Example MSE object used in the vignette
Rcontrol

Harvest Control Rule using prior for intrinsic rate of increase
Rcontrol2

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

An data-limited method which sets a slot limit
SnapMSE

Example MSE object used in the vignette
Tplot

A trade-off plot for an MSE object
TAC

Calculate TAC recommendations for more than one MP
wormplot

Biomass wormplot.
writeCSV

Internal function to write CSVs for objects
Fratio_CC

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

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

~~ Methods for Function initialize ~~
Input

Function to run a set of input control methods
ITe10

Index Target Effort-Based 10
LBSPRSim

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

Apply LBSPR model to time-series of catch-at-length
ITe5

Index Target Effort-Based 5
FMSYref75

A reference FMSY method that fishes at three quarters of FMSY (uses perfect information about FMSY)
FMSYref50

A reference FMSY method that fishes at half of FMSY (uses perfect information about FMSY)
LtargetE4

A management procedure that incrementally adjusts the Effort to reach a target mean length in catches.
Islope1

A management procedure that incrementally adjusts the TAC to maintain a constant CPUE or relative abundance index.
Islope4

A management procedure that incrementally adjusts the TAC to maintain a constant CPUE or relative abundance index.
IT10

Index Target 10
IT5

Index Target 5
LstepCC1

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

Class "lmmodel"
LstepCE1

A management procedure that incrementally adjusts the TAC according to the mean length of recent catches.
LstepCC4

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

Class "MSE"
NAor0

Is a value NA or zero.
OptFun

Objective function for LBSPR methods
runInMP

Runs input control MPs on a DLM_data object.
ourMSE

Example MSE object used in the vignette
runMSE

Run a Management Strategy Evaluation
SBT1

SBT simple MP
SBT2

SBT complex MP
makePerf

Convert a OM object to one without observation or process error
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).
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
ourReefFish

Example data object
plot-methods

~~ Methods for Function plot ~~
Required

What methods need what data
replic8

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

Surplus production based catch-limit modifier
TradePlot

Generic Trade-off Plot
SPMSY

Catch trend Surplus Production MSY MP