AAVY                    Performance Metric: Probability AAVY < 0.2
Albacore                Albacore Stock
Atlantic_mackerel       Atlantic_mackerel Data
AvC                     Average Catch
AvC_MLL                 Average Catch with a size limit
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
Blue_shark              Blue_shark Stock
Bluefin_tuna            Bluefin_tuna Stock
Bluefin_tuna_WAtl       Bluefin_tuna_WAtl Stock
Butterfish              Butterfish Stock
CC1                     Constant catch management procedure of Geromont
                        and Butterworth (2014)
CC4                     Constant catch management procedure of Geromont
                        and Butterworth (2014)
COSEWIC_plot            COSEWIC forward projection plot
CSRA                    Catch at size reduction analysis
CSRAfunc                Optimization function for CSRA
Can                     What management procedures can be applied to
                        this Data object?
Cant                    What management procedures can't be applied to
                        this DLM data object
China_rockfish          China_rockfish Data
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
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)
Converge                Check Convergence
Cplot                   Plot the median biomass and yield relative to
                        last historical year
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
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
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-package         Data-Limited Methods Toolkit
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
Data-class              Class "Data"
DataDescription         DataDescription
DataInit                Initialize an empty Data workbook or CSV
Data_xl                 Read in Data object from Excel spreadsheet
DecE_Dom                DecE_Dom Fleet
DecE_HDom               DecE_HDom Fleet
DecE_NDom               DecE_NDom Fleet
DepF                    Depletion Corrected Fratio
DynF                    Dynamic Fratio MP
EtargetLopt             Effort MP: adjust effort up/down if mean length
                        above/below Ltarget
Example_datafile        Example_datafile Data
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)
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
FlatE_Dom               FlatE_Dom Fleet
FlatE_HDom              FlatE_HDom Fleet
FlatE_NDom              FlatE_NDom Fleet
Fleet-class             Class "Fleet"
FleetDescription        FleetDescription
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
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
Gulf_blue_tilefish      Gulf_blue_tilefish Data
HDAAC                   Hybrid Depletion Adjusted Average Catch
Herring                 Herring Stock
ICI                     Index Confidence Interval (ICI) MP by Jardim et
                        al. (2015)
ICI2                    Less Precautionary Index Confidence Interval
                        (ICI) MP by Jardim et al. (2015)
IOTC_plot               Indian Ocean Tuna Commission trade-off plot
IT10                    Index Target 10
IT5                     Index Target 5
ITM                     Index Target based on natural mortality rate
ITe10                   Index Target Effort-Based 10
ITe5                    Index Target Effort-Based 5
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
Input                   Function to run a set of input control methods
Iratio                  Mean index ratio MP from Jardim et al. 2015
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
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
Itarget1_MPA            A example mixed control MP that uses the
                        Itarget1 output control MP together with a
                        spatial closure.
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
Kplot                   KOBE plot: a projection by projection plot of
                        F/FMSY and B/BMSY
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.
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
LTY                     Performance Metric: Probability Long-Term Yield
                        > 0.5 Relative Yield
LinInterp               Linear interpolation of a y value at level xlev
                        based on a vector x and y
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.
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.
MCD                     Mean Catch Depletion
MCD4010                 Mean Catch Depletion
ML2D                    Depletion and F estimation from mean length of
                        catches
MPStats                 Calculate Statistics for MP Performance
MPtype                  Management Procedure Type
MRnoreal                An marine reserve in area 1 with no spatial
                        reallocation of fishing effort
MRreal                  A marine reserve in area 1 with full
                        reallocation of fishing effort
MSE-class               Class "MSE"
Mackerel                Mackerel Stock
NAor0                   Is a value NA or zero.
NFref                   No Fishing Reference MP
NOAA_plot               National Oceanographic and Atmospheric
                        Administration default plot 1
Needed                  Data needed to get MPs running
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                Overages Imp
P10                     Performance Metric: Probability B > 0.1 BMSY
P100                    Performance Metric: Probability B > BMSY
P50                     Performance Metric: Probability B > 0.5 BMSY
PMobj-class             An object for storing data for analysis using
                        data-limited methods
POF                     Performance Metric: Probability F < FMSY
PWhisker                Performance Whisker Plot
Perfect_Imp             Perfect_Imp Imp
Perfect_Info            Perfect_Info Obs
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
Range                   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
Rec-class               Class "Rec"
Red_snapper             Red_snapper Data
Replace                 Replace an existing Stock, Fleet, Obs, or Imp
                        object
Required                What management procedures need what data
Rockfish                Rockfish Stock
SBT1                    SBT simple MP
SBT2                    SBT complex MP
SPMSY                   Catch trend Surplus Production MSY MP
SPSRA                   Surplus Production Stock Reduction Analysis
SPSRA_ML                Surplus Production Stock Reduction Analysis
                        using a mean-length estimate of current stock
                        depletion
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
SRopt                   Function that returns a stochastic estimate of
                        steepness given observed stock recruitment data
SS2DLM                  Reads MLE estimates from Stock Synthesis file
                        structure into an operating model using package
                        r4ss
SS2Data                 Reads data Stock Synthesis file structure into
                        an data object using package r4ss
STY                     Performance Metric: Probability Short-Term
                        Yield > 0.5 Relative Yield
SampleCpars             Sample custom pars
SampleFleetPars         Sample Fleet Parameters
SampleImpPars           Sample Implementation Error Parameters
SampleObsPars           Sample Observation Parameters
SampleStockPars         Sample Stock parameters
Sense                   Sensitivity analysis
SimulatedData           SimulatedData Data
Simulation_1            Simulation_1 Data
SketchFun               Manually map the historical relative fishing
                        effort trajectory.
Snapper                 Snapper Stock
Sole                    Sole Stock
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
Target_All_Fish         Target_All_Fish Fleet
Targeting_Small_Fish    Targeting_Small_Fish Fleet
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
VOI                     Calculate Value Of Information
VOI2                    Calculate Value Of Information 2
VOIplot                 Yet another Value of Information Plot
XL2Data                 Import a Data object from Excel file
XL2OM                   Load OM from Excel file
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
Yield                   Performance Metric: Average Yield
alphaconv               Calculate alpha parameter for beta distribution
                        from mean and standard deviation
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
betaconv                Calculate beta parameter for beta distribution
                        from mean and standard deviation
boxplot.Data            Boxplot of TAC recommendations
calcMean                Calculate Mean Probabilty
calcProb                Calculate Probabilty
checkMSE                Check that MSE object includes all slots
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
curE75                  Fishing at 75 per cent of current effort levels
cv                      Calculate CV from vector of values
derive_beta_par         This function reduces the CV by 5 per cent
                        until steepness values can be sampled without
                        error
dnormal                 Double-normal selectivity curve
fetch.file.names        Reads iSCAM Data, Control and Projection files
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
getFref3                Calculate Reference Yield
getGpars                Extracts growth parameters from a SS3 r4ss
                        replist
getclass                get object class
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
hist2                   Wrapper for histogram function
iSCAM2DLM               Reads MLE estimates from iSCAM file structure
                        into an operating model
iSCAM2Data              Reads data from iSCAM file structure into a
                        DLMtool Data object
iSCAMcomps              Combines all iSCAM age composition data across
                        fleets
iSCAMinds               Combines indices into a single index using
                        linear modelling
initialize-methods      ~~ Methods for Function 'initialize' ~~
joinMSE                 Join multiple MSE objects together
label.class-class       Label class union for performance metric
                        objects
load.iscam.files        Reads iSCAM files into a hierarchical R list
                        object
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 NEW
matlenlim2              A data-limited method in which fishing
                        vulnerability is set slightly higher than the
                        maturity curve
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.
movdistil               Simplified a multi-area transition matrix into
                        the best 2 x 2 representation
movfit_Rcpp             Rcpp version of the Optimization function that
                        returns the squared difference between user
                        specified and calculated movement parameters.
negcorlogspace          A function that samples multivariate normal
                        (logspace) variables
optBH                   Wrapper for estimating stock recruitment
                        parameters from resampled stock-recruitment
                        data
optCPU                  Determine optimal number of cpus
optMSY                  Optimize yield for a single simulation
optQ                    Optimize q for a single simulation
ourReefFish             Example data object
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
prob.class-class        Prob class union for performance metric objects
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
replic8                 Enlarge (replicate) a DLM data object to create
                        an additional dimension for simulation /
                        sensitivity testing
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
sample_steepness2       Sample steepness given mean and cv
sampy                   Sample vector
sdconv                  Get log normal standard deviation from
                        transformed space mean and standard deviation
setup                   Setup parallel processing
show,PMobj-method       Show the output of a PM
show,Rec-method         Show the output of a single MP recommendation
simYears                Simulate population dynamics for historical
                        years
slotlim                 An data-limited method which sets a slot limit
summary,Data-method     Summary of Data object
summary,MSE-method      Summary of MSE object
tdlnorm                 Calculate density of log-normally distributed
                        random numbers
testOM                  testOM OM
trlnorm                 Generate log-normally distributed random
                        numbers
updateMSE               Update an MSE object with new slots
userguide               Open the DLMtool User Guide
validcpars              Valid custom parameters (cpars)
wormplot                Biomass wormplot
writeCSV                Internal function to write CSVs for objects
