Function reference • MSEtool Functions

All functions
`ASAP2OM()` `ASAP2Data()`	Convert ASAP 3 assessments into an operating model
`Assess2MOM()`	Reads bootstrap estimates from a stock assessment model into a multi-fleet operating model.
`Assess2OM()` `VPA2OM()`	Reads bootstrap estimates from a stock assessment model (including VPA) into an operating model. `Assess2OM` is identical to `VPA2OM`.
`Awatea2OM()`	Reads MCMC estimates from Awatea (Paul Starr) processed r file structure into an operating model
`CALsimp()`	Simplifies the CAL slot of data object
`Can()` `Cant()` `DLMdiag()` `Needed()`	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
`ChooseEffort()` `ChooseM()` `ChooseSelect()`	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
`Atlantic_mackerel` `China_rockfish` `Cobia` `Example_datafile` `Gulf_blue_tilefish` `ourReefFish` `Red_snapper` `Simulation_1`	Data class objects
`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
`Dom()`	Determine dominate MPs
`FMSYref()` `FMSYref50()` `FMSYref75()` `NFref()` `curEref()`	Reference management procedures
`Fease()`	MP feasibility diagnostic
`DecE_Dom` `DecE_HDom` `DecE_NDom` `FlatE_Dom` `FlatE_HDom` `FlatE_NDom` `Generic_DecE` `Generic_FlatE` `Generic_Fleet` `Generic_IncE` `IncE_HDom` `IncE_NDom` `Low_Effort_Non_Target` `Target_All_Fish` `Targeting_Small_Fish`	Fleet class objects
`Fleet-class`	Class `'Fleet'`
`FleetDescription`	FleetDescription
`Hist-class`	Class `'Hist'`
`HistDescription`	HistDescription
`Overages` `Perfect_Imp`	Imp class objects
`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()` `predictLH()`	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'`
`Albacore_TwoFleet`	MOM class objects
`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
`NIL()`	Item in list: get the list values from a list of lists
`NOAA_plot()`	National Oceanographic and Atmospheric Administration default plot 1
`testOM`	OM class objects
`OM-class`	Class `'OM'`
`OMDescription`	OMDescription
`OMdoc()`	Generate OM Documentation Report
`OMexample()`	Copy example OM XL and OM Documentation
`OMinit()`	Initialize Operating Model
`Generic_Obs` `Imprecise_Biased` `Imprecise_Unbiased` `Perfect_Info` `Precise_Biased` `Precise_Unbiased`	Obs class objects
`Obs-class`	Class `'Obs'`
`ObsDescription`	ObsDescription
`PMLimit()` `PMObj()`	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
`P10()` `P50()` `P100()` `PNOF()` `LTY()` `STY()` `Yield()` `AAVY()` `AAVE()`	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()` `plot_SS2MOM()` `SS2OM()` `SSMOM2OM()` `plot_SS2OM()` `MOM_agg_fleets()`	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
`SimulatedData`	SimulatedData Data
`SketchFun()`	Manually map the historical relative fishing effort trajectory.
`Albacore` `Blue_shark` `Bluefin_tuna` `Bluefin_tuna_WAtl` `Butterfish` `Herring` `Mackerel` `Porgy` `Rockfish` `Snapper` `Sole` `Toothfish`	Stock class objects
`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()` `Tplot()` `Tplot2()` `Tplot3()` `NOAA_plot2()`	Generic Trade-Plot Function
`Turing()` `TuringMOM()`	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 WHAM (Wood's Hole Assessment 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
`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()` `addMPs()` `joinMSE()` `joinHist()` `updateMSE()`	Utility functions for MSE objects
`cparscheck()`	Internal function for checking that the `OM@cpars` is formatted correctly
`dnormal()`	Double-normal selectivity curve
`expandHerm()`	Expand the Herm list in SexPars to a matrix of fractions at age
`getDataList()`	Get part of an MP specific data-list
`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()` `R0conv()` `SRalphaconv()` `SRbetaconv()`	Stock recruit parameterization
`hist2()`	Wrapper for histogram function
`load.iscam.files()` `fetch.file.names()` `read.report.file()` `read.data.file()` `read.control.file()` `read.projection.file()` `read.par.file()` `read.mcmc()`	Reads iSCAM files into a hierarchical R list object
`iSCAM2OM()` `iSCAM2Data()`	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` `initialize,Data-method` `initialize,Fleet-method` `initialize,MSE-method` `initialize,Obs-method` `initialize,OM-method` `initialize,Stock-method` `initialize` `initialize,Fease-method` `initialize,DLM_general-method`	~~ 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()` `print(<Rel>)` `predict(<Rel>)` `simulate(<Rel>)`	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)
`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
`SimulateMOM()` `ProjectMOM()` `multiMSE()`	Run a multi-fleet multi-stock Management Strategy Evaluation
`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>,<missing>)`	Standard plot for an object of class MOM
`plot(<MSE>)`	Plot MSE object
`plot(<pars>)` `plot(<Stock>)` `plot(<Fleet>)` `plot(<Obs>)` `plot(<Imp>)` `plot(<Hist>)` `plot(<OM>)`	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
`replic8()`	Enlarge (replicate) a DLM data object to create an additional dimension for simulation / sensitivity testing
`runCOSEWIC()` `COSEWIC_Pplot()` `COSEWIC_Dplot()` `COSEWIC_Blow()` `COSEWIC_Hplot()` `COSEWIC_report()` `COSEWIC_tab()` `COSEWIC_tab_formatted()`	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
`Simulate()` `Project()` `runMSE()`	Run a Management Strategy Evaluation
`setup()`	Setup parallel processing
`show(<PMobj>)`	Show the output of a PM
`show(<Rec>)`	Show the output of a single MP recommendation
`simCAA()`	Simulate Catch-at-Age Data
`simCAL()`	Simulate Catch-at-Length Data
`simmov()` `plot_mov()`	Calculates movement matrices from user inputs
`summary(<Data>)`	Summary of Data object
`summary(<MMSE>)`	Summary of MMSE object
`summary(<MSE>)`	Summary of MSE object
`tinyErr()`	Remove observation, implementation, and process error
`validcpars()`	Valid custom parameters (cpars)
`wormplot()`	Biomass wormplot
`writeCSV()`	Internal function to write CSVs for objects

Reference

All functions