# Data-Limited Methods Toolkit

## Documentation for package ‘DLMtool’ version 5.0.2

- 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 X Y

DLMtool-package | Data-Limited Methods Toolkit

## -- A --

AAVY | Performance Metric: Probability AAVY < 0.2
Albacore | Albacore Stock
alphaconv | Calculate alpha parameter for beta distribution from mean and standard deviation
Atlantic_mackerel | Atlantic_mackerel 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
Blow_opt | Blow internal parallel optimization function
Bluefin_tuna | Bluefin_tuna Stock
Bluefin_tuna_WAtl | Bluefin_tuna_WAtl Stock
Blue_shark | Blue_shark Stock
boxplot.Data | Boxplot of TAC recommendations
boxplot.MSE | Boxplot of MP performance from MSE object
Butterfish | Butterfish Stock

## -- C --

calcMean | Calculate Mean Probabilty
CalcOutput | Apply output control recommendations and calculate population dynamics
calcProb | Calculate Probabilty
Can | What data-limited methods can be applied to this 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 Data
ChkDatNA | Check Data object is valid for a MP
ChkObj | Check that a DLM object is valid
ChooseEffort | Manually map the historical relative fishing effort trajectory.
ChooseM | Manually map natural mortality at age or size.
ChooseSelect | Manually choose the historical selectivity pattern
Cobia | Cobia Data
compplot | Generic comparison plot for simulation testing of Stochastic SRA method
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
COSEWIC_plot | COSEWIC forward projection plot
cparscheck | Internal function of runMSE for checking that the OM slot cpars slot is formatted correctly
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
Data-class | Class "Data"
DataDescription | DataDescription
Data_xl | Read in Data object from Excel spreadsheet
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
derive_beta_par | This function reduces the CV by 5 per cent until steepness values can be sampled without error
DFO_hist | Deparment of Fisheries and Oceans historical plot
DFO_plot | Deparment of Fisheries and Oceans trade-off plot
DFO_plot2 | Deparment of Fisheries and Oceans default plot 2
DFO_proj | Deparment of Fisheries and Oceans projection plot
DLMDataDir | Directory of the installed package on your computer
DLMextra | Load more data from DLMextra package
DLMtool | Data-Limited Methods Toolkit
dnormal | Double-normal selectivity curve
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 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-class | Class "Fease"
Fease_xl | Read in feasibility parameters from Excel spreadsheet
Feasibility | Feasibility Fease
Feasibility2 | Feasibility2 Fease
fetch.file.names | Reads iSCAM Data, Control and Projection files
FlatE_Dom | FlatE_Dom Fleet
FlatE_HDom | FlatE_HDom Fleet
FlatE_NDom | FlatE_NDom Fleet
Fleet-class | Class "Fleet"
FleetDescription | FleetDescription
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)
ForceCor | Forces correlation among operating model parameters for M, K, Linf and L50
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 Obs
genLenComp | Generate length composition of catch
getAFC | Calculate age at first capture from length at first capture and growth
getBH | Predict Beverton-Holt recruitment and return fit to S-R observations
getBlow | Blow parallel optimization function
getclass | get object class
getFMSY3 | Calculate FMSY and related metrics using Rcpp code
getFref3 | Calculate Reference Yield
getGpars | Extracts growth parameters from a SS3 r4ss replist
getmov2 | Optimization function to find a movement model that matches user specified movement characteristics modified for Rcpp.
getq3 | optimize for catchability (q)
getsel | Calculate selectivity curve
Gulf_blue_tilefish | Gulf_blue_tilefish Data

## -- H --

HDAAC | Hybrid Depletion Adjusted Average Catch
Herring | Herring Stock
hist2 | Wrapper for histogram function

## -- I --

ICI | Index Confidence Interval (ICI) MP by Jardim et al. (2015)
ICI2 | Less Precautionary Index Confidence Interval (ICI) MP by Jardim et al. (2015)
Imp-class | Class "Imp"
ImpDescription | ImpDescription
Imprecise_Biased | Imprecise_Biased Obs
Imprecise_Unbiased | Imprecise_Unbiased Obs
IncE_HDom | IncE_HDom Fleet
IncE_NDom | IncE_NDom Fleet
initialize | ~~ Methods for Function 'initialize' ~~
initialize-method | ~~ Methods for Function 'initialize' ~~
initialize-methods | ~~ Methods for Function 'initialize' ~~
Input | Function to run a set of input control methods
InputRec-class | Class "InputRec"
IOTC_plot | Indian Ocean Tuna Commission trade-off plot
Iratio | Mean index ratio MP from Jardim et al. 2015
iSCAM2Data | Reads data from iSCAM file structure into a DLMtool Data object
iSCAM2DLM | Reads MLE estimates from iSCAM file structure into an operating model
iSCAMcomps | Combines all iSCAM age composition data across fleets
iSCAMinds | Combines indices into a single index using linear modelling
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.
label.class-class | Label class union for performance metric objects
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
LinInterp | Linear interpolation of a y value at level xlev based on a vector x and y
load.iscam.files | Reads iSCAM files into a hierarchical R list object
Low_Effort_Non_Target | Low_Effort_Non_Target Fleet
Lratio_BHI | Mean length-based indicator MP of Jardim et al. 2015 using Beverton-Holt invariant M/K ratio = 1.5 and assumes FMSY = M.
Lratio_BHI2 | The more general version of the mean length-based indicator MP of Jardim et al. 2015.
LSRA | Estimates R0 using SRA to match current F estimates and avoid penalities for low stock sizes
LSRA2 | Alternative version of LSRA that's a wrapper for LSRA_opt to return the right type of output (mode) using sapply
LSRA_MCMC_sim | Internal SRA MCMC CPP code
LSRA_opt | Internal estimation function for LSRA and LSRA2 functions
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.
LTY | Performance Metric: Probability Long-Term Yield > 0.5 Relative Yield

## -- 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 retention 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
movdistil | Simplified a multi-area transition matrix into the best 2 x 2 representation
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"

## -- N --

NAor0 | Is a value NA or zero.
Needed | Data needed to get MPs running
negcorlogspace | A function that samples multivariate normal (logspace) variables
NFref | No Fishing Reference MP
NOAA_plot | National Oceanographic and Atmospheric Administration default plot 1

## -- O --

Obs-class | Class "Obs"
ObsDescription | ObsDescription
OM-class | Class "OM"
OMDescription | OMDescription
OMdoc | Generate OM Documentation Report
OMexample | Copy example OM XL and OM Documentation
OMinit | Initialize Operating Model
OM_xl | Read in operating model parameters from Excel spreadsheet
optBH | Wrapper for estimating stock recruitment parameters from resampled stock-recruitment data
optMSY | Optimize yield for a single simulation
optQ | Optimize q for a single simulation
ourReefFish | Example data object
Overages | Overages Imp

## -- P --

P10 | Performance Metric: Probability B > 0.1 BMSY
P100 | Performance Metric: Probability B > BMSY
P50 | Performance Metric: Probability B > 0.5 BMSY
Perfect_Imp | Perfect_Imp Imp
Perfect_Info | Perfect_Info Obs
plot-method | Plot Data object
plot-method | Plot MSE object
plot.OM | Plot the operating model (OM) object parameters
plotFleet | Plot the Fleet object parameters
plotFun | Print out plotting functions
plotImp | Plot the Implementation object parameters
plotM | Plot M-at-Age and Size
plotObs | Plot the Observation object parameters
plotOFL | A generic OFL plot for NOAA use
plotSelect | Plot the vulnerability and retention curves
plotStock | Plot the Stock object parameters
PMobj-class | An object for storing data for analysis using data-limited methods
POF | Performance Metric: Probability F < FMSY
popdyn | Population dynamics model
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 Obs
Precise_Unbiased | Precise_Unbiased Obs
prob.class-class | Prob class union for performance metric objects
PWhisker | Performance Whisker Plot

## -- 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
read.control.file | Reads iSCAM control file
read.data.file | Reads iSCAM dat file
read.mcmc | Reads iSCAM mcmc output files
read.par.file | Reads iSCAM parameter file
read.projection.file | Reads iSCAM projection file
read.report.file | Reads iSCAM Rep file
Red_snapper | Red_snapper Data
Replace | Replace an existing Stock, Fleet, Obs, or Imp object
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 Data object.
runMSE | Run a Management Strategy Evaluation
runMSErobust | Run a Management Strategy Evaluation

## -- S --

Sam | Conduct stock assessment
SampleCpars | Sample custom pars
SampleFleetPars | Sample Fleet Parameters
SampleImpPars | Sample Implementation Error Parameters
SampleObsPars | Sample Observation Parameters
SampleStockPars | Sample Stock parameters
sample_steepness2 | Sample steepness given mean and cv
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
setup | Setup parallel processing
show-method | Show the output of a PM
Simulation_1 | Simulation_1 Data
simYears | Simulate population dynamics for historical years
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
SRAcomp | Plot simulation test of Stochastic SRA method
SRAsim | Simulates catch at age and catch history data for testing SRA methods
SRopt | Function that returns a stochastic estimate of steepness given observed stock recruitment data
SS2Data | Reads data Stock Synthesis file structure into an data object using package r4ss
SS2DLM | Reads MLE estimates from Stock Synthesis file structure into an operating model using package r4ss
StochasticSRA | Stochastic SRA construction of operating models
StochasticSRAcpp | Stochastic SRA construction of operating models
Stock-class | Class "Stock"
StockDescription | StockDescription
STY | Performance Metric: Probability Short-Term Yield > 0.5 Relative Yield
Sub | Subset MSE object by management procedure (MP) or simulation.
SubCpars | Subset an OM cpars slot
SubOM | Subset a Stock, Fleet, Obs, or Imp object from an OM object
summary-method | Summary of 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
testOM | testOM OM
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
Tplot3 | Test Trade-Off Plot
TradePlot | Generic Trade-off Plot
trlnorm | Generate log-normally distributed random numbers

## -- U --

updateMSE | Update an MSE object with new slots
userguide | Open the DLMtool User Guide

## -- V --

validcpars | Valid custom parameters (cpars)
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

## -- X --

XL2OM | Load OM from Excel file

## -- Y --

Yield | Performance Metric: Average Yield
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