ASAP2OM                 Convert ASAP 3 assessments into an operating
                        model
Albacore                Stock class objects
Albacore_TwoFleet       MOM class objects
Assess2MOM              Reads bootstrap estimates from a stock
                        assessment model into a multi-fleet operating
                        model.
Assess2OM               Reads bootstrap estimates from a stock
                        assessment model (including VPA) into an
                        operating model. 'Assess2OM' is identical to
                        'VPA2OM'.
Atlantic_mackerel       Data class objects
Awatea2OM               Reads MCMC estimates from Awatea (Paul Starr)
                        processed r file structure into an operating
                        model
BAM2MOM                 Import a multi-stock, multi-fleet OM from a BAM
                        object
CALsimp                 Simplifies the CAL slot of data object
Can                     Identify management procedures (MPs) based on
                        data availability
CheckDuplicate          Check for duplicated MPs names
CheckMPs                Check that specified MPs are valid and will run
                        on MSEtool::SimulatedData
CheckOM                 Check OM object is complete
Choose                  Manually map parameters for the historical
                        period of operating model
CombineMMP              Create a blank MP recommendations object (class
                        Rec) of the right dimensions
Converge                Check Convergence
Cos_thresh_tab          Current default thresholds for COSEWIC
                        satisficing
Cplot                   Plot the median biomass and yield relative to
                        last historical year
DFO_bar                 Department of Fisheries and Oceans stock status
                        bar plot
DFO_hist                Department of Fisheries and Oceans historical
                        plot
DFO_plot                Department of Fisheries and Oceans trade-off
                        plot
DFO_plot2               Department of Fisheries and Oceans default plot
                        2
DFO_proj                Department of Fisheries and Oceans projection
                        plot
DFO_quant               Department 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
Data-class              Class "Data"
Data2csv                Converts a Data object into a .csv data file
DataDescription         DataDescription
DataDir                 Directory of the data in the installed package
                        on your computer
DataInit                Initialize Data Input Files
DataSlots               DataSlots
Data_xl                 Read in Data object from Excel spreadsheet
DecE_Dom                Fleet class objects
Dom                     Determine dominate MPs
Emp                     A flexible empirical management procedure.
FMSYref                 Reference management procedures
Fease                   MP feasibility diagnostic
Fleet-class             Class "Fleet"
FleetDescription        FleetDescription
Generic_Obs             Obs class objects
Herm-int                Internal Herm functions
Hist-class              Class "Hist"
HistDescription         HistDescription
Imp-class               Class "Imp"
ImpDescription          ImpDescription
Input                   Function to run a set of input control methods
Kplot                   KOBE plot: a projection by projection plot of
                        F/FMSY and B/BMSY
LH2OM                   Predict missing life-history parameters
LHdatabase              LHdatabase
Lag_Data                Lag the time-series slots in a 'Data' object by
                        a specified number of time-steps
ML2D                    Depletion and F estimation from mean length of
                        catches
MMSE-class              Class "MMSE"
MOM-class               Class "MOM"
MPCalcsNAs              Fill any NAs arising from MPCalcs
                        (hermaphroditism mode)
MPtype                  Management Procedure Type
MSE-class               Class "MSE"
MSEDescription          MSEDescription
MSEextra                Load more data from MSEextra package
MSYCalcs                Internal function to calculate MSY Reference
                        Points
NIL                     Item in list: get the list values from a list
                        of lists
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
RealFease               MP feasibility diagnostic using real data
Rec-class               Class "Rec"
Replace                 Replace an existing Stock, Fleet, Obs, or Imp
                        object
Report                  Generate a Data Report
ReqData                 ReqData
Required                What management procedures need what data
SIL                     Slot in list: get the slot values from a list
                        of objects
SS2Data                 Reads data Stock Synthesis file structure into
                        a Data object using package r4ss
SS2DataMOM              Reads data Stock Synthesis file structure into
                        a nested Data object analogous with multiMSE
SS2MOM                  Import Stock Synthesis to MOM (2-sex
                        multi-fleet) or OM (single-sex, single-fleet)
SSBrefplot              Plot Spawning stock biomass and reference
                        points for both historical and projected period
Sense                   Sensitivity analysis
Simulate                Run a Management Strategy Evaluation
SimulateMOM             Run a multi-fleet multi-stock Management
                        Strategy Evaluation
SimulatedData           SimulatedData Data
SketchFun               Manually map the historical relative fishing
                        effort trajectory.
Splot                   Standard MSE projection plot
Stock-class             Class "Stock"
StockDescription        StockDescription
Sub                     Subset MSE object by management procedure (MP)
                        or simulation.
SubCpars                Subset the cpars slot in an operating model
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
TEG                     Tom's expand grid
Taxa_Table              Taxa_Table
Thresh_tab              Current default thresholds for DFO satisficing
TradePlot               Generic Trade-Plot Function
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
WHAM2OM                 Takes a fitted SAM model and samples historical
                        population and fishing dynamics from the MLE
                        fit and variance-covariance matrix.
XL2Data                 Import a Data object from Excel file
XL2Fleet                Import Fleet Object from Excel file
XL2OM                   Load OM from Excel file
XL2Stock                Import Stock Object from Excel file
addMMPs                 Utility functions for multiMSE objects
applyMMP                Apply multi Management Procedures (class MMP)
                        to a hierarchical list of Data class objects
applyMP                 Apply Management Procedures to an object of
                        class Data
avail                   What objects of this class are available
boxplot.Data            Boxplot of TAC recommendations
calcRefYield            Calculate Reference Yield
checkMSE                Utility functions for MSE objects
cparscheck              Internal function for checking that the
                        'OM@cpars' is formatted correctly
dnormal                 Double-normal selectivity curve
doHCR                   Hockey Stick Harvest control rule that modifies
                        TAC.
doIfreq                 Create indices that are sampled at various
                        frequencies
doRec                   Calculate a management recommendation given
                        constraints
getDataList             Get part of an MP specific data-list
getMP                   Search R session for MP
getclass                get object class
getfirstlev             Extract the first dimension of a hierarchical
                        list of recommendation objects
getmov2                 Optimization function to find a movement model
                        that matches user specified movement
                        characteristics modified for Rcpp.
getnIVs                 Count independent variables for a MICE
                        relationship at position x in a Rel list
getsel                  Calculate selectivity curve
hconv                   Stock recruit parameterization
hist2                   Wrapper for histogram function
iSCAM                   Reads iSCAM files into a hierarchical R list
                        object
iSCAM2OM                Reads MPD or MCMC estimates and data 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 (** Deprecated **)
initialize-methods      ~~ Methods for Function 'initialize' ~~
joinData                Join Data objects present in a list
join_plots              Plot several plots with a shared legend
ldim                    Dimensions of a hierarchical list object
makeMOM                 Utility for making multi-OMs
makeRel                 MICE relationships for multi-OM
makeTransparent         Make colors transparent
makemov                 Calculates movement matrices from user inputs
                        for fraction in each area (fracs) and
                        probability of staying in areas (prob)
makemov2                Calculates movement matrices from user inputs
                        for fraction in each area (fracs) the relative
                        fraction moving to other areas, plus a mean
                        probability of staying in any given area.
movestockCPP            Apply the movement model to the stock for one
                        time-step
movfit_Rcpp             Rcpp version of the Optimization function that
                        returns the squared difference between user
                        specified and calculated movement parameters.
multiData               Combine data among fleets
multiDataS              Combine data among stocks
multidebug              A basic comparison of runMSE output (MSE) and
                        multiMSE (MMSE)
optCPU                  Determine optimal number of cpus
plot.Data               Plot Data object
plot.MMSE               Standard plot for an object of class MMSE
                        (multi MSE)
plot.MOM                Standard plot for an object of class MOM
plot.MSE                Plot MSE object
plot.pars               Plot Operating Model Object
plotFun                 Print out plotting functions
plotOFL                 A generic OFL plot for NOAA use
plotRel                 Plot a relationship between stocks
plotmulti               A basic SSB plot for debugging runMSE output
plotquant               A fairly tidy time-series quantile plot
print.multiHist         Print method for 'multiHist' objects
quantile_plot           A quantile plot
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
select_MP               Select DataList for an MP from 'MMSE@PPD'
setup                   Setup parallel processing
show,PMobj-method       Show the output of a PM
show,Rec-method         Show the output of a single MP recommendation
show-MSEtool            Show MSEtool S4 objects
simCAA                  Simulate Catch-at-Age Data
simCAL                  Simulate Catch-at-Length Data
simmov                  Calculates movement matrices from user inputs
simmov2                 Calculates movement matrices from user
                        specified distribution among other areas
smoothy                 General purpose polynomial smoother
summary,Data-method     Summary of Data object
summary,MMSE-method     Summary of MMSE object
summary,MSE-method      Summary of MSE object
testOM                  OM class objects
tinyErr                 Remove observation, implementation, and process
                        error
tune_MP                 Tune MP
validcpars              Valid custom parameters (cpars)
wormplot                Biomass wormplot
writeCSV                Internal function to write CSVs for objects
