# Data-Limited Methods Toolkit

## Documentation for package ‘DLMtool’ version 3.2.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I J K L M N O P Q R S T U V W Y

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 --

barplot.MSE | Plot a barplot of MSE results
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
boxplot.DLM_data | Boxplot of TAC recommendations
boxplot.MSE | Boxplot of MP performance from MSE object

## -- 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)
Cplot | Plot the median biomass and yield relative to last historical year
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

## -- E --

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

## -- 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
Jplot | Joint probability plot

## -- 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
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.
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
minlenLopt1 | This input control sets the minimum length of fish caught to a fraction of the length that maximises the biomass, Lopt.
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.
MPStats | Calculate Statistics for MP Performance
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' ~~
plotFun | Print out plotting functions
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
Splot | Scatter plot of B/BMSY or B/B0 and F/FMSY
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