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DLMtool (version 3.2.2)

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

3.2.2

License

GPL-2

Maintainer

Tom Carruthers

Last Published

December 27th, 2016

Functions in DLMtool (3.2.2)

Can

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

Boxplot of MP performance from MSE object
Cant

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

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

What objects of this class are available
boxplot.DLM_data

Boxplot of TAC recommendations
BK_CC

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

Plot a barplot of MSE results
CC1

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

Comparison plots for individual simulations
CSRA

Catch at size reduction analysis
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)
CC4

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

Optimization function for CSRA
CheckConverg

MSE convergence diagnostic
Cplot

Plot the median biomass and yield relative to last historical year
ChooseEffort

Manually choose the historical relative fishing effort trajectory.
CompSRA

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

Depletion Corrected Average Catch
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
DAAC

Depletion Adjusted Average Catch
DCAC_40

Depletion Corrected Average Catch assuming 40 per cent stock depletion
DBSRA

Depletion-Based Stock Reduction Analysis
DBSRA4010

Depletion-Based Stock Reduction Analysis paired with 40-10 harvest control rule
curE75

Fishing at 75 per cent of current effort levels
curE

Fishing at current effort levels
DBSRA_40

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

Class "DLM_general"
DLM_fease-class

Class "DLM_fease"
DDe75

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

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

Delay - Difference Stock Assessment with UMSY and MSY leading
DCAC4010

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

How dominant is an MP?
DLMtool-package

Data-Limited Methods Toolkit
Fease

MP feasibility diagnostic
Fleet-class

Class "Fleet"
DepF

Depletion Corrected Fratio
DLM_data-class

Class "DLM_data"
FMSYref75

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

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

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

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

Hybrid Depletion Adjusted Average Catch
GB_CC

Geromont and Butterworth Constant Catch Harvest Control Rule
Fratio4010

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

~~ Methods for Function initialize ~~
KalmanFilter

Kalman filter and Rauch-Tung-Striebel smoother
Kplot

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

Demographic FMSY method using catch-curve analysis to estimate recent Z
Islope4

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

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

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

G-control MP
joinMSE

Join multiple MSE objects together
IT10

Index Target 10
Jplot

Joint probability plot
LBSPR_ItEff

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

Geromont and Butterworth index slope Harvest Control Rule
LBSPR_ItSel

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

Geromont and Butterworth target CPUE and catch MP
ItargetE1

A management procedure that incrementally adjusts the effort to reach a target CPUE / relative abundance index.
L95target

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.
L2A

Length to age conversion
LstepCC1

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.
makePerf

Convert a OM object to one without observation or process error
LBSPRSim

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

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

Class "lmmodel"
NOAA_plot

National Oceanographic and Atmospheric Administration default plot 1
minlenLopt1

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

No Fishing Reference MP
MCD4010

Mean Catch Depletion
Observation-class

Class "Observation"
OM_xl

Read in operating model parameters from Excel spreadsheet
replic8

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

Directory of the installed package on your computer
DLMdat

Data and Operating model objects
DD4010

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

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

What methods need what data
getq

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

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

Function to run a set of input control methods
Islope1

A management procedure that incrementally adjusts the TAC to maintain a constant CPUE or relative abundance index.
ITe5

Index Target Effort-Based 5
ITM

Index Target based on natural mortality rate
ItargetE4

A management procedure that incrementally adjusts the Effort to reach a target CPUE / relative abundance index.
ITe10

Index Target Effort-Based 10
LstepCE1

A management procedure that incrementally adjusts the TAC according to the mean length of recent catches.
FMSYref50

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

A reference FMSY method (uses perfect information about FMSY)
DTe40

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

Optimization routine for LBSPR methods
LstepCE2

A management procedure that incrementally adjusts the Effort according to the mean length of recent catches.
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
LtargetE4

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

Class "MSE"
ourMSE

Example MSE object used in the vignette
runInMP

Runs input control MPs on a DLM_data object.
ourReefFish

Example data object
runMSE

Run a Management Strategy Evaluation
Sense

Sensitivity analysis
SetRecruitCycle

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

Demographic FMSY method
DynF

Dynamic Fratio MP
DTe50

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

Read in feasibility parameters from Excel spreadsheet
Fratio

An FMSY/M ratio method
Fratio_ML

An FMSY/M ratio MP that uses a mean length estimator of recent Z
IT5

Index Target 5
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.
LBSPR

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

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

Mean Catch Depletion
matlenlim2

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

Surplus production based catch-limit modifier
Splot

Scatter plot of B/BMSY or B/B0 and F/FMSY
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)
Sub

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

Class "Stock"
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
VOIplot

Yet another Value of Information Plot
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).
MPStats

Calculate Statistics for MP Performance
MRnoreal

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

Robust Virtual Population Analysis
OM-class

Class "OM"
OptFun

Objective function for LBSPR methods
SPSRA_ML

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

Biomass wormplot.
SPSRA

Surplus Production Stock Reduction Analysis
writeCSV

Internal function to write CSVs for objects
plotFun

Print out plotting functions
plot-methods

~~ Methods for Function plot ~~
Rcontrol2

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

Harvest Control Rule using prior for intrinsic rate of increase
SBT1

SBT simple MP
SBT2

SBT complex MP
summary-methods

~~ Methods for Function summary ~~
YPR

Yield Per Recruit analysis to get FMSY proxy F01
TAC

Calculate TAC recommendations for more than one MP
NAor0

Is a value NA or zero.
Ltarget4

A management procedure that incrementally adjusts the TAC to reach a target mean length in catches.
Ltarget1

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

A generic OFL plot for NOAA use
Needed

Data needed to get MPs running
PorgMSE

Example MSE object used in the vignette
runMSErobust

Run a Management Strategy Evaluation
TradePlot

Generic Trade-off Plot
updateMSE

Update an MSE object with new slots
SPMSY

Catch trend Surplus Production MSY MP
SPslope

Slope in surplus production MP
Sam

Conduct stock assessment
VOI

Calculate Value Of Information
YPR_CC

Yield Per Recruit analysis to get FMSY proxy F01 paired to a naive catch curve estimate of recent Z
VOI2

Calculate Value Of Information 2
YPR_ML

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