Albacore                Stock class objects
Atlantic_mackerel       Data class objects
AvC                     Average Catch
AvC_MLL                 Average Catch with a size limit
BK                      Beddington and Kirkwood life-history MP
CALsimp                 Simplifies the CAL slot of data object
CC                      Age-based Catch Curve
CC1                     Geromont and Butterworth (2015) Constant Catch
Can                     Identify management procedures (MPs) based on
                        data availability
ChkObj                  Check that a DLM object is valid
Choose                  Manually map parameters for the historical
                        period of operating model
CompSRA                 Age-Composition Stock-Reduction Analysis
Converge                Check Convergence
Cos_thresh_tab          Current default thresholds for COSEWIC
                        satificing
Cplot                   Plot the median biomass and yield relative to
                        last historical year
DBSRA                   Depletion-Based Stock Reduction Analysis
DCACs                   Depletion Corrected Average Catch
DD                      Delay - Difference Stock Assessment
DDe                     Effort-based Delay - Difference Stock
                        Assessment
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-package         Data-Limited Methods Toolkit
DOM                     How dominant is an MP?
DTe40                   Effort searching MP aiming for a fixed stock
                        depletion
Data-class              Class "Data"
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
DecE_Dom                Fleet class objects
DynF                    Dynamic Fratio MP
EtargetLopt             Effort Target Optimum Length
FMSYref                 Reference management procedures
Fadapt                  Adaptive Fratio
Fdem                    Demographic FMSY method
Fease                   MP feasibility diagnostic
Fleet-class             Class "Fleet"
FleetDescription        FleetDescription
ForceCor                Forces correlation among operating model
                        parameters for M, K, Linf and L50
Fratio                  FMSY/M ratio methods
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_Obs             Obs class objects
Growth2OM               Generate bootstrapped estimates of von
                        Bertalanffy growth parameters from
                        length-at-age data
Hist-class              Class "Hist"
ICI                     Index Confidence Interval
IOTC_plot               Indian Ocean Tuna Commission trade-off plot
IT5                     Iterative Index Target MP
ITM                     Index Target based on natural mortality rate
ITe5                    Index Target Effort-Based
Imp-class               Class "Imp"
ImpDescription          ImpDescription
Input                   Function to run a set of input control methods
Iratio                  Mean Index Ratio
Islope1                 Index Slope Tracking MP
Itarget1                Incremental Index Target MP
Itarget1_MPA            Itarget1 with an MPA
ItargetE1               Incremental Index Target MP - Effort-Based A
                        management procedure that incrementally adjusts
                        the fishing effort to reach a target CPUE /
                        relative abundance index
Kplot                   KOBE plot: a projection by projection plot of
                        F/FMSY and B/BMSY
LBSPR                   Length-Based SPR MPs
LH2OM                   Predict missing life-history parameters
LHdatabase              LHdatabase
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
LW2OM                   Estimate length-weight parameters from data
Lratio_BHI              Mean length-based indicator MP of Jardim et al.
                        2015
LstepCC1                Step-wise Constant Catch
LstepCE1                Step-wise Constant Effort
Ltarget1                Length Target TAC MP
LtargetE1               Length Target TAE MP
MCD                     Mean Catch Depletion
ML2D                    Depletion and F estimation from mean length of
                        catches
MPStats                 Calculate Statistics for MP Performance
MPtype                  Management Procedure Type
MRreal                  Spatial closure and allocation management
                        procedures
MSE-class               Class "MSE"
MSEDescription          MSEDescription
NOAA_plot               National Oceanographic and Atmospheric
                        Administration default plot 1
OM-class                Class "OM"
OMDescription           OMDescription
OMdoc                   Generate OM Documentation Report
OMexample               Copy example OM XL and OM Documentation
OMinit                  Initialize Operating Model
Obs-class               Class "Obs"
ObsDescription          ObsDescription
Overages                Imp class objects
PMLimit                 Create a table of Performance Limits and
                        Performance Objectives
PMobj-class             An object for storing data for analysis using
                        data-limited methods
PWhisker                Performance Whisker Plot
PerformanceMetric       Performance Metrics Methods
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
Rcontrol                Intrinsic rate of Increase MP
RealFease               MP feasibility diagnostic using real data
Rec-class               Class "Rec"
Replace                 Replace an existing Stock, Fleet, Obs, or Imp
                        object
ReqData                 ReqData
Required                What management procedures need what data
SBT1                    SBT simple MP
SPMSY                   Catch trend Surplus Production MSY MP
SPSRA                   Surplus Production Stock Reduction Analysis
SPmod                   Surplus production based catch-limit modifier
SPslope                 Slope in surplus production MP
SRAcomp                 Plot simulation test of Stochastic SRA method
SRAsim                  Simulates catch at age and catch history data
                        for testing SRA methods
Sense                   Sensitivity analysis
SimulatedData           SimulatedData Data
SketchFun               Manually map the historical relative fishing
                        effort trajectory.
StochasticSRA           Stochastic SRA construction of operating models
StochasticSRAcpp        Stochastic SRA construction of operating models
Stock-class             Class "Stock"
StockDescription        StockDescription
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
TAC                     Calculate TAC recommendations for more than one
                        MP
TACfilter               TAC Filter
Thresh_tab              Current default thresholds for DFO satificing
Tplot_old               Trade-off plots for an MSE object
TradePlot               Generic Trade-Plot Function
TradePlot_old           Generic Trade-off Plot
Turing                  Turing Test
Uses                    Find the Management Procedures that use a
                        particular data slot
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
XL2Data                 Import a Data object from Excel file
XL2OM                   Load OM from Excel file
YPR                     Yield Per Recruit analysis to get FMSY proxy
                        F01
applyMP                 Apply Management Procedures to an object of
                        class Data
avail                   What objects of this class are available
barplot.MSE             Plot a barplot of MSE results
boxplot.Data            Boxplot of TAC recommendations
cheatsheets             Opens the DLMtool Cheat-Sheets (requires
                        internet connection)
checkMSE                Utility functions for MSE objects
compplot                Generic comparison plot for simulation testing
                        of Stochastic SRA method
condmet                 Condition met?
cparscheck              Internal function of runMSE for checking that
                        the OM slot cpars slot is formatted correctly
curE                    Fishing at current effort levels
dnormal                 Double-normal selectivity curve
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
hist2                   Wrapper for histogram function
initialize-methods      ~~ Methods for Function 'initialize' ~~
joinData                Join Data objects present in a list
join_plots              Plot several plots with a shared legend
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
movfit_Rcpp             Rcpp version of the Optimization function that
                        returns the squared difference between user
                        specified and calculated movement parameters.
optCPU                  Determine optimal number of cpus
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
plotOFL                 A generic OFL plot for NOAA use
plotObs                 Plot the Observation object parameters
plotSelect              Plot the vulnerability and retention curves
plotStock               Plot the Stock object parameters
replic8                 Enlarge (replicate) a DLM data object to create
                        an additional dimension for simulation /
                        sensitivity testing
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
setup                   Setup parallel processing
show,PMobj-method       Show the output of a PM
show,Rec-method         Show the output of a single MP recommendation
simCAA                  Simulate Catch-at-Age Data
simCAL                  Simulate Catch-at-Length Data
summary,Data-method     Summary of Data object
summary,MSE-method      Summary of MSE object
testOM                  testOM OM
tinyErr                 Remove observation, implementation, and process
                        error
userguide               Open the DLMtool User Guide
validcpars              Valid custom parameters (cpars)
wormplot                Biomass wormplot
writeCSV                Internal function to write CSVs for objects
