# Data-Limited Methods Toolkit

## Documentation for package ‘DLMtool’ version 3.2.3

- DESCRIPTION file.

## Help Pages

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

DLMtool-package | Data-Limited Methods Toolkit

## -- A --

Albacore | Albacore Stock
alphaconv | Calculate alpha parameter for beta distribution from mean and standard deviation
Atlantic_mackerel | Atlantic_mackerel DLM_data
avail | What objects of this class are available
AvC | Average Catch

## -- B --

barplot.MSE | Plot a barplot of MSE results
betaconv | Calculate beta parameter for beta distribution from mean and standard deviation
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
Bluefin_tuna | Bluefin_tuna Stock
Bluefin_tuna_WAtl | Bluefin_tuna_WAtl Stock
Blue_shark | Blue_shark Stock
boxplot.DLM_data | Boxplot of TAC recommendations
boxplot.MSE | Boxplot of MP performance from MSE object
Butterfish | Butterfish Stock

## -- 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
checkMSE | Check that MSE object includes all slots
China_rockfish | China_rockfish DLM_data
ChooseEffort | Manually map the historical relative fishing effort trajectory.
ChooseSelect | Manually choose the historical selectivity pattern
Cobia | Cobia DLM_data
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)
condmet | Condition met?
Converge | Check Convergence
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
cv | Calculate CV from vector of values

## -- 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
DecE_Dom | DecE_Dom Fleet
DecE_HDom | DecE_HDom Fleet
DecE_NDom | DecE_NDom Fleet
DepF | Depletion Corrected Fratio
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"
DOM | How dominant is an MP?
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
Example_datafile | Example_datafile DLM_data

## -- 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
Feasibility | Feasibility DLM_fease
Feasibility2 | Feasibility2 DLM_fease
FlatE_Dom | FlatE_Dom Fleet
FlatE_HDom | FlatE_HDom Fleet
FlatE_NDom | FlatE_NDom Fleet
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
Generic_DecE | Generic_DecE Fleet
Generic_FlatE | Generic_FlatE Fleet
Generic_fleet | Generic_fleet Fleet
Generic_IncE | Generic_IncE Fleet
Generic_obs | Generic_obs Observation
genLenComp | Generate length composition of catch
getAFC | Calculate age at first capture from length at first capture and growth
getclass | get object class
getmov | Optimization function to find a movement model that matches user specified movement characteristics.
getmov2 | Optimization function to find a movement model that matches user specified movement characteristics modified for Rcpp.
Gulf_blue_tilefish | Gulf_blue_tilefish DLM_data

## -- H --

HDAAC | Hybrid Depletion Adjusted Average Catch
Herring | Herring Stock

## -- I --

Imprecise_Biased | Imprecise_Biased Observation
Imprecise_Unbiased | Imprecise_Unbiased Observation
IncE_Dom | IncE_Dom Fleet
IncE_HDom | IncE_HDom Fleet
IncE_NDom | IncE_NDom Fleet
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 --

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 the Length-based SPR model to DLMtool Data Object
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"
Low_Effort_Non_Target | Low_Effort_Non_Target Fleet
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 --

Mackerel | Mackerel Stock
makePerf | Convert a OM object to one without observation or process error
makeTransparent | Make colors transparent
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
mconv | Get log normal mean from transformed space mean and standard deviation
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. (deprecated: now in Rcpp)
movfit_Rcpp | Rcpp version of the 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"
mypars | mypars DLM_general

## -- 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
ourReefFish | Example data object

## -- P --

Perfect_Info | Perfect_Info Observation
plot-method | Plot DLM_data object
plot-method | Plot MSE object
plotFun | Print out plotting functions
plotOFL | A generic OFL plot for NOAA use
Porgy | Porgy Stock
Pplot | A projection by projection plot of F/FMSY and B/BMSY
Pplot2 | A projection by projection plot of F/FMSY, B/BMSY, B/B0, and yield
Precise_Biased | Precise_Biased Observation
Precise_Unbiased | Precise_Unbiased Observation

## -- R --

Range | Standardize values
range01 | Standardize values
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
Red_snapper | Red_snapper DLM_data
replic8 | Enlarge (replicate) a DLM data object to create an additional dimension for simulation / sensitivity testing
Required | What methods need what data
Rockfish | Rockfish Stock
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
sampy | Sample vector
SBT1 | SBT simple MP
SBT2 | SBT complex MP
sdconv | Get log normal standard deviation from transformed space mean and standard deviation
Sense | Sensitivity analysis
SetRecruitCycle | Function to calculate cyclic recruitment pattern given user-specified values of period and amplitude.
setup | Setup parallel processing
Simulation_1 | Simulation_1 DLM_data
SketchFun | Manually map the historical relative fishing effort trajectory.
slotlim | An data-limited method which sets a slot limit
Snapper | Snapper Stock
Sole | Sole Stock
Splot | Scatter plot of B/BMSY or B/B0 and F/FMSY for lastYrs
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 | Summary of DLM_data object
summary-method | Summary of MSE object

## -- T --

TAC | Calculate TAC recommendations for more than one MP
TACfilter | TAC Filter
Targeting_Small_Fish | Targeting_Small_Fish Fleet
Target_All_Fish | Target_All_Fish Fleet
tdlnorm | Calculate density of log-normally distributed random numbers
Toothfish | Toothfish Stock
Tplot | A trade-off plot for an MSE object
Tplot2 | A shorter version of the plot method for MSEs that just shows the overall trade-offs
TradePlot | Generic Trade-off Plot
trlnorm | Generate log-normally distributed random numbers

## -- 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

## -- 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