Data-Limited Methods Toolkit


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Documentation for package ‘DLMtool’ version 3.2.1

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DLMtool-package Data-Limited Methods Toolkit

-- A --

avail What objects of this class are available
AvC An MP where the TAC is average historical catch

-- B --

BK Beddington and Kirkwood life-history MP (simple version)
BK_CC Beddington and Kirkwood life-history method combined with catch curve analysis
BK_ML Beddington and Kirkwood life-history analysis with mean-length estimator of current abundance

-- C --

Can What data-limited methods can be applied to this DLM_data object?
Cant What methods can't be applied to this DLM data object
CC1 Constant catch management procedure of Geromont and Butterworth (2014)
CC4 Constant catch management procedure of Geromont and Butterworth (2014)
CheckConverg MSE convergence diagnostic
ChooseEffort Manually choose the historical relative fishing effort trajectory.
ChooseSelect Manually choose the historical selectivity pattern.
comp Comparison plots for individual simulations
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)
CSRA Catch at size reduction analysis
CSRAfunc Optimization function for CSRA
curE Fishing at current effort levels
curE75 Fishing at 75 per cent of current effort levels

-- D --

DAAC Depletion Adjusted Average Catch
DBSRA Depletion-Based Stock Reduction Analysis
DBSRA4010 Depletion-Based Stock Reduction Analysis paired with 40-10 harvest control rule
DBSRA_40 Depletion-Based Stock Reduction Analysis assuming 40 per cent stock depletion
DBSRA_ML Depletion-Based Stock Reduction Analysis using mean length estimator of stock depletion
DCAC Depletion Corrected Average Catch
DCAC4010 Depletion Corrected Average Catch paired with the 40-10 rule
DCAC_40 Depletion Corrected Average Catch assuming 40 per cent stock depletion
DCAC_ML Depletion-Based Stock Reduction Analysis using mean-length estimator of current depletion
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
DDe Effort control version of DD - Delay - Difference Stock Assessment with UMSY and MSY leading
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
DepF Depletion Corrected Fratio
DLMdat Data and Operating model objects
DLMDataDir Directory of the installed package on your computer
DLMtool Data-Limited Methods Toolkit
DLM_data-class Class '"DLM_data"'
DLM_fease-class Class '"DLM_fease"'
DLM_general-class Class '"DLM_general"'
DOM How dominant is an MP?
DoOpt Optimization routine for LBSPR methods
DTe40 Effort searching MP aiming for 40 per cent stock depletion.
DTe50 Effort searching MP aiming for 50 per cent stock depletion.
DynF Dynamic Fratio MP

-- F --

Fadapt An adaptive MP that uses trajectory in inferred suplus production and fishing mortality rate to update a TAC
Fdem Demographic FMSY method
Fdem_CC Demographic FMSY method using catch-curve analysis to estimate recent Z
Fdem_ML Demographic FMSY method that uses mean length data to estimate recent Z
Fease MP feasibility diagnostic
Fease_xl Read in feasibility parameters from Excel spreadsheet
Fleet-class Class '"Fleet"'
FMSYref A reference FMSY method (uses perfect information about FMSY)
FMSYref50 A reference FMSY method that fishes at half of FMSY (uses perfect information about FMSY)
FMSYref75 A reference FMSY method that fishes at three quarters of FMSY (uses perfect information about FMSY)
Fratio An FMSY/M ratio method
Fratio4010 An FMSY/M ratio method paired with the 40-10 rule
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

-- G --

GB_CC Geromont and Butterworth Constant Catch Harvest Control Rule
GB_slope Geromont and Butterworth index slope Harvest Control Rule
GB_target Geromont and Butterworth target CPUE and catch MP
Gcontrol G-control MP
getAFC Calculate age at first capture from length at first capture and growth
getmov Optimization function to find a movement model that matches user specified movement characteristics.
getq Optimization function that find the catchability (q where F=qE) value required to get to user-specified stock depletion (current biomass / unfished biomass)

-- H --

HDAAC Hybrid Depletion Adjusted Average Catch

-- I --

initialize-method ~~ Methods for Function 'initialize' ~~
initialize-methods ~~ Methods for Function 'initialize' ~~
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.
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
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.
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.
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.
ITe10 Index Target Effort-Based 10
ITe5 Index Target Effort-Based 5
ITM Index Target based on natural mortality rate

-- J --

joinMSE Join multiple MSE objects together

-- K --

KalmanFilter Kalman filter and Rauch-Tung-Striebel smoother
Kplot KOBE plot: a projection by projection plot of F/FMSY and B/BMSY

-- L --

L2A Length to age conversion
LBSPR Apply LBSPR model to time-series of catch-at-length
LBSPRSim Per-Recruit Length-Based Spawning Potential Ratio Simulation Model
LBSPR_ItEff Length-based SPR model with HCR that iteratively adjusts Effort
LBSPR_ItSel Length-based SPR model with HCR that iteratively adjusts Selectivity.
LBSPR_ItTAC Length-based SPR model with HCR that iteratively adjusts TAC
lmmodel-class Class '"lmmodel"'
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.
LstepCE1 A management procedure that incrementally adjusts the TAC according to the mean length of recent catches.
LstepCE2 A management procedure that incrementally adjusts the Effort according to the mean length of recent catches.
Ltarget1 A management procedure that incrementally adjusts the TAC to reach a target mean length in catches.
Ltarget4 A management procedure that incrementally adjusts the TAC 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.
LtargetE4 A management procedure that incrementally adjusts the Effort to reach a target mean length in catches.

-- M --

makePerf Convert a OM object to one without observation or process error
matlenlim A data-limited method in which fishing vulnerability is set according to the maturity curve
matlenlim2 A data-limited method in which fishing vulnerability is set slightly higher than the maturity curve
MCD Mean Catch Depletion
MCD4010 Mean Catch Depletion
ML2D Depletion and F estimation from mean length of catches
movfit Optimization function that returns the squared difference between user specified and calculated movement parameters.
MRnoreal An marine reserve in area 1 with no spatial reallocation of fishing effort
MRreal An marine reserve in area 1 with full reallocation of fishing effort
MSE-class Class '"MSE"'

-- N --

NAor0 Is a value NA or zero.
Needed Data needed to get MPs running
NFref No Fishing Reference MP
NOAA_plot National Oceanographic and Atmospheric Administration default plot 1

-- O --

Observation-class Class '"Observation"'
OM-class Class '"OM"'
OM_xl Read in operating model parameters from Excel spreadsheet
OptFun Objective function for LBSPR methods
ourMSE Example MSE object used in the vignette
ourReefFish Example data object

-- P --

plot-method ~~ Methods for Function 'plot' ~~
plot-methods ~~ Methods for Function 'plot' ~~
plotOFL A generic OFL plot for NOAA use
PorgMSE Example MSE object used in the vignette
Pplot A projection by projection plot of F/FMSY and B/BMSY

-- Q --

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)

-- R --

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
replic8 Enlarge (replicate) a DLM data object to create an additional dimension for simulation / sensitivity testing
Required What methods need what data
runInMP Runs input control MPs on a DLM_data object.
runMSE Run a Management Strategy Evaluation
runMSErobust Run a Management Strategy Evaluation

-- S --

Sam Conduct stock assessment
SBT1 SBT simple MP
SBT2 SBT complex MP
Sense Sensitivity analysis
SetRecruitCycle Function to calculate cyclic recruitment pattern given user-specified values of period and amplitude.
slotlim An data-limited method which sets a slot limit
SnapMSE Example MSE object used in the vignette
SPmod Surplus production based catch-limit modifier
SPMSY Catch trend Surplus Production MSY MP
SPslope Slope in surplus production MP
SPSRA Surplus Production Stock Reduction Analysis
SPSRA_ML Surplus Production Stock Reduction Analysis using a mean-length estimate of current stock depletion
Stock-class Class '"Stock"'
Sub Subset MSE object by management procedure (MP) or simulation.
summary-method ~~ Methods for Function 'summary' ~~
summary-methods ~~ Methods for Function 'summary' ~~

-- T --

TAC Calculate TAC recommendations for more than one MP
Tplot A trade-off plot for an MSE object
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).
TradePlot Generic Trade-off Plot

-- U --

updateMSE Update an MSE object with new slots

-- V --

VOI Calculate Value Of Information
VOI2 Calculate Value Of Information 2
VOIplot Yet another Value of Information Plot
VPA Robust Virtual Population Analysis

-- W --

wormplot Biomass wormplot.
writeCSV Internal function to write CSVs for objects

-- Y --

YPR Yield Per Recruit analysis to get FMSY proxy F01
YPR_CC Yield Per Recruit analysis to get FMSY proxy F01 paired to a naive catch curve estimate of recent Z
YPR_ML Yield Per Recruit analysis to get FMSY proxy F01 paired with a mean-length estimate of current stock size