# Data-Limited Methods Toolkit

## Documentation for package ‘DLMtool’ version 5.3

- 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 X Y

DLMtool-package | Data-Limited Methods Toolkit

## -- A --

AAVY | Performance Metrics Methods
Albacore | Stock class objects
applyMP | Apply Management Procedures to an object of class Data
Atlantic_mackerel | Data class objects
avail | What objects of this class are available
AvC | Average Catch
AvC_MLL | Average Catch with a size limit

## -- B --

barplot.MSE | Plot a barplot of MSE results
BK | Beddington and Kirkwood life-history MP
BK_CC | Beddington and Kirkwood life-history MP
BK_ML | Beddington and Kirkwood life-history MP
Bluefin_tuna | Stock class objects
Bluefin_tuna_WAtl | Stock class objects
Blue_shark | Stock class objects
boxplot.Data | Boxplot of TAC recommendations
Butterfish | Stock class objects

## -- C --

CALsimp | Simplifies the CAL slot of data object
Can | Identify management procedures (MPs) based on data availability
Cant | Identify management procedures (MPs) based on data availability
CC | Age-based Catch Curve
CC1 | Geromont and Butterworth (2015) Constant Catch
CC2 | Geromont and Butterworth (2015) Constant Catch
CC3 | Geromont and Butterworth (2015) Constant Catch
CC4 | Geromont and Butterworth (2015) Constant Catch
CC5 | Geromont and Butterworth (2015) Constant Catch
cheatsheets | Opens the DLMtool Cheat-Sheets (requires internet connection)
checkMSE | Utility functions for MSE objects
China_rockfish | Data class objects
ChkObj | Check that a DLM object is valid
Choose | Manually map parameters for the historical period of operating model
ChooseEffort | Manually map parameters for the historical period of operating model
ChooseM | Manually map parameters for the historical period of operating model
ChooseSelect | Manually map parameters for the historical period of operating model
Cobia | Data class objects
compplot | Generic comparison plot for simulation testing of Stochastic SRA method
CompSRA | Age-Composition Stock-Reduction Analysis
CompSRA4010 | Age-Composition Stock-Reduction Analysis
condmet | Condition met?
Converge | Check Convergence
COSEWIC_Blow | COSEWIC MSE run using the correct MPs and projected time horizon
COSEWIC_Dplot | COSEWIC MSE run using the correct MPs and projected time horizon
COSEWIC_Hplot | COSEWIC MSE run using the correct MPs and projected time horizon
COSEWIC_Pplot | COSEWIC MSE run using the correct MPs and projected time horizon
COSEWIC_report | COSEWIC MSE run using the correct MPs and projected time horizon
COSEWIC_tab | COSEWIC MSE run using the correct MPs and projected time horizon
COSEWIC_tab_formatted | COSEWIC MSE run using the correct MPs and projected time horizon
Cos_thresh_tab | Current default thresholds for COSEWIC satificing
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
curE | Fishing at current effort levels
curE75 | Fishing at current effort levels

## -- D --

DAAC | Depletion Corrected Average Catch
Data-class | Class "Data"
Data-class-objects | Data class objects
Data2csv | Converts a Data object into a .csv data file
DataDescription | DataDescription
DataInit | Initialize an empty Data workbook or CSV
Data_xl | Read in Data object from Excel spreadsheet
DBSRA | Depletion-Based Stock Reduction Analysis
DBSRA4010 | Depletion-Based Stock Reduction Analysis
DBSRA_40 | Depletion-Based Stock Reduction Analysis
DCAC | Depletion Corrected Average Catch
DCAC4010 | Depletion Corrected Average Catch
DCACs | Depletion Corrected Average Catch
DCAC_40 | Depletion Corrected Average Catch
DCAC_ML | Depletion Corrected Average Catch
DD | Delay - Difference Stock Assessment
DD4010 | Delay - Difference Stock Assessment
DDe | Effort-based Delay - Difference Stock Assessment
DDe75 | Effort-based Delay - Difference Stock Assessment
DDes | Effort-based Delay - Difference Stock Assessment
DecE_Dom | Fleet class objects
DecE_HDom | Fleet class objects
DecE_NDom | Fleet class objects
DepF | FMSY/M ratio methods
DFO_bar | Deparment of Fisheries and Oceans stock status bar plot
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
DFO_quant | Deparment of Fisheries and Oceans biomass quantile plot
DFO_report | Create a standard DFO MSE report
DFO_spider | DFO performance spider plot (top three MPs)
DFO_tab | Create a standard DFO performance table
DFO_tab_formatted | A formatted version of the standard DFO performance plot, color coded by thresholds
DLMDataDir | Directory of the installed package on your computer
DLMenv | DLMenv blank environment
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 a fixed stock depletion
DTe50 | Effort searching MP aiming for a fixed stock depletion
DynF | Dynamic Fratio MP

## -- E --

EtargetLopt | Effort Target Optimum Length
Example_datafile | Data class objects

## -- F --

Fadapt | Adaptive Fratio
Fdem | Demographic FMSY method
Fdem_CC | Demographic FMSY method
Fdem_ML | Demographic FMSY method
Fease | MP feasibility diagnostic
FlatE_Dom | Fleet class objects
FlatE_HDom | Fleet class objects
FlatE_NDom | Fleet class objects
Fleet-class | Class "Fleet"
Fleet-class-objects | Fleet class objects
FleetDescription | FleetDescription
FMSYref | Reference management procedures
FMSYref50 | Reference management procedures
FMSYref75 | Reference management procedures
ForceCor | Forces correlation among operating model parameters for M, K, Linf and L50
Fratio | FMSY/M ratio methods
Fratio4010 | FMSY/M ratio methods
Fratio_CC | FMSY/M ratio methods
Fratio_ML | FMSY/M ratio methods

## -- 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 | Fleet class objects
Generic_FlatE | Fleet class objects
Generic_Fleet | Fleet class objects
Generic_IncE | Fleet class objects
Generic_Obs | Obs class objects
getclass | get object class
getmov2 | Optimization function to find a movement model that matches user specified movement characteristics modified for Rcpp.
getsel | Calculate selectivity curve
Growth2OM | Generate bootstrapped estimates of von Bertalanffy growth parameters from length-at-age data
Gulf_blue_tilefish | Data class objects

## -- H --

HDAAC | Depletion Corrected Average Catch
Herring | Stock class objects
Hist-class | Class "Hist"
hist2 | Wrapper for histogram function

## -- I --

ICI | Index Confidence Interval
ICI2 | Index Confidence Interval
Imp-class | Class "Imp"
Imp-class-objects | Imp class objects
ImpDescription | ImpDescription
Imprecise_Biased | Obs class objects
Imprecise_Unbiased | Obs class objects
IncE_HDom | Fleet class objects
IncE_NDom | Fleet class objects
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
IOTC_plot | Indian Ocean Tuna Commission trade-off plot
Iratio | Mean Index Ratio
Islope1 | Index Slope Tracking MP
Islope2 | Index Slope Tracking MP
Islope3 | Index Slope Tracking MP
Islope4 | Index Slope Tracking MP
IT10 | Iterative Index Target MP
IT5 | Iterative Index Target MP
Itarget1 | Incremental Index Target MP
Itarget1_MPA | Itarget1 with an MPA
Itarget2 | Incremental Index Target MP
Itarget3 | Incremental Index Target MP
Itarget4 | Incremental Index Target MP
ItargetE1 | Incremental Index Target MP - Effort-Based A management procedure that incrementally adjusts the fishing effort to reach a target CPUE / relative abundance index
ItargetE2 | Incremental Index Target MP - Effort-Based A management procedure that incrementally adjusts the fishing effort to reach a target CPUE / relative abundance index
ItargetE3 | Incremental Index Target MP - Effort-Based A management procedure that incrementally adjusts the fishing effort to reach a target CPUE / relative abundance index
ItargetE4 | Incremental Index Target MP - Effort-Based A management procedure that incrementally adjusts the fishing effort to reach a target CPUE / relative abundance index
ITe10 | Index Target Effort-Based
ITe5 | Index Target Effort-Based
ITM | Index Target based on natural mortality rate

## -- J --

joinData | Join Data objects present in a list
joinMSE | Utility functions for MSE objects
join_plots | Plot several plots with a shared legend

## -- K --

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

## -- L --

L95target | Length Target TAC MP
LBSPR | Length-Based SPR MPs
LBSPR_MLL | Length-Based SPR MPs
LH2OM | Predict missing life-history parameters
LHdatabase | LHdatabase
Low_Effort_Non_Target | Fleet class objects
Lratio_BHI | Mean length-based indicator MP of Jardim et al. 2015
Lratio_BHI2 | Mean length-based indicator MP of Jardim et al. 2015
Lratio_BHI3 | 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 | Step-wise Constant Catch
LstepCC2 | Step-wise Constant Catch
LstepCC3 | Step-wise Constant Catch
LstepCC4 | Step-wise Constant Catch
LstepCE1 | Step-wise Constant Effort
LstepCE2 | Step-wise Constant Effort
Ltarget1 | Length Target TAC MP
Ltarget2 | Length Target TAC MP
Ltarget3 | Length Target TAC MP
Ltarget4 | Length Target TAC MP
LtargetE1 | Length Target TAE MP
LtargetE4 | Length Target TAE MP
LTY | Performance Metrics Methods
LW2OM | Estimate length-weight parameters from data

## -- M --

Mackerel | Stock class objects
makeMeanMP | Create an MP that averages the results of multiple MPs
makePerf | Convert a OM object to one without observation or process error
makeTransparent | Make colors transparent
matlenlim | Size limit management procedures
matlenlim2 | Size limit management procedures
MCD | Mean Catch Depletion
MCD4010 | Mean Catch Depletion
minlenLopt1 | Size limit management procedures
ML2D | Depletion and F estimation from mean length of catches
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
MPtype | Management Procedure Type
MRnoreal | Spatial closure and allocation management procedures
MRreal | Spatial closure and allocation management procedures
MSE-class | Class "MSE"
MSEDescription | MSEDescription

## -- N --

Needed | Identify management procedures (MPs) based on data availability
NFref | Reference management procedures
NOAA_plot | National Oceanographic and Atmospheric Administration default plot 1
NOAA_plot2 | Generic Trade-Plot Function

## -- O --

Obs-class | Class "Obs"
Obs-class-objects | Obs class objects
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
optCPU | Determine optimal number of cpus
ourReefFish | Data class objects
Overages | Imp class objects

## -- P --

P10 | Performance Metrics Methods
P100 | Performance Metrics Methods
P50 | Performance Metrics Methods
Perfect_Imp | Imp class objects
Perfect_Info | Obs class objects
PerformanceMetric | Performance Metrics Methods
plot.Data | Plot Data object
plot.MSE | 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
plotMPA | Plot the Historical Spatial Closures
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
PMLimit | Create a table of Performance Limits and Performance Objectives
PMObj | Create a table of Performance Limits and Performance Objectives
PMobj-class | An object for storing data for analysis using data-limited methods
PNOF | Performance Metrics Methods
Porgy | Stock class objects
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 | Obs class objects
Precise_Unbiased | Obs class objects
predictLH | Predict missing life-history parameters
PWhisker | Performance Whisker Plot

## -- R --

Rcontrol | Intrinsic rate of Increase MP
Rcontrol2 | Intrinsic rate of Increase MP
RealFease | MP feasibility diagnostic using real data
Rec-class | Class "Rec"
Red_snapper | Data class objects
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
ReqData | ReqData
Required | What management procedures need what data
Rockfish | Stock class objects
runCOSEWIC | COSEWIC MSE run using the correct MPs and projected time horizon
runInMP | Runs input control MPs on a Data object.
runMP | Run a Management Procedure
runMSE | Run a Management Strategy Evaluation
runMSErobust | Run a Management Strategy Evaluation

## -- S --

SBT1 | SBT simple MP
SBT2 | SBT simple MP
Sense | Sensitivity analysis
setup | Setup parallel processing
show-method | Show the output of a PM
show-method | Show the output of a single MP recommendation
simCAA | Simulate Catch-at-Age Data
simCAL | Simulate Catch-at-Length Data
SimulatedData | SimulatedData Data
Simulation_1 | Data class objects
SketchFun | Manually map the historical relative fishing effort trajectory.
slotlim | Size limit management procedures
Snapper | Stock class objects
Sole | Stock class objects
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
SRAcomp | Plot simulation test of Stochastic SRA method
SRAsim | Simulates catch at age and catch history data for testing SRA methods
StochasticSRA | Stochastic SRA construction of operating models
StochasticSRAcpp | Stochastic SRA construction of operating models
Stock-class | Class "Stock"
Stock-class-objects | Stock class objects
StockDescription | StockDescription
STY | Performance Metrics Methods
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 | Fleet class objects
Target_All_Fish | Fleet class objects
testOM | testOM OM
Thresh_tab | Current default thresholds for DFO satificing
tinyErr | Remove observation, implementation, and process error
Toothfish | Stock class objects
Tplot | Generic Trade-Plot Function
Tplot2 | Generic Trade-Plot Function
Tplot2_old | Trade-off plots for an MSE object
Tplot3 | Generic Trade-Plot Function
Tplot_old | Trade-off plots for an MSE object
TradePlot | Generic Trade-Plot Function
TradePlot_old | Generic Trade-off Plot
Turing | Turing Test

## -- U --

updateMSE | Utility functions for MSE objects
userguide | Open the DLMtool User Guide
Uses | Find the Management Procedures that use a particular data slot

## -- V --

validcpars | Valid custom parameters (cpars)
VOI | Calculate Value Of Information
VOI2 | Calculate Value Of Information 2
VOIplot | Yet another Value of Information Plot
VOIplot2 | Value of Information Plot using PM functions

## -- W --

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

## -- X --

XL2Data | Import a Data object from Excel file
XL2OM | Load OM from Excel file

## -- Y --

Yield | Performance Metrics Methods
YPR | Yield Per Recruit analysis to get FMSY proxy F01
YPR_CC | Yield Per Recruit analysis to get FMSY proxy F01
YPR_ML | Yield Per Recruit analysis to get FMSY proxy F01