| alphaconv | Calculate parameters for beta distribution from mean and... |
| applyMMP | Apply multi Management Procedures (class MMP) to a... |
| applyMP | Apply Management Procedures to an object of class Data |
| ASAP2OM | Convert ASAP 3 assessments into an operating model |
| Assess2MOM | Reads bootstrap estimates from a stock assessment model into... |
| Assess2OM | Reads bootstrap estimates from a stock assessment model... |
| avail | What objects of this class are available |
| Awatea2OM | Reads MCMC estimates from Awatea (Paul Starr) processed r... |
| BlankSelPlot | Internal function to create a blank plot for mapping... |
| Blow_opt | Blow internal parallel optimization function |
| boxplot.Data | Boxplot of TAC recommendations |
| calcMean | Calculate Mean Probability |
| CalcMPDynamics | Calculate population dynamics from MP recommendation |
| calcProb | Calculate Probability |
| calcRefYield | Calculate Reference Yield |
| CalculateQ | Optimize for catchability (q) |
| CALsimp | Simplifies the CAL slot of data object |
| Can | Identify management procedures (MPs) based on data... |
| char.log-class | Class union for isRel slot |
| CheckDuplicate | Check for duplicated MPs names |
| CheckMPs | Check that specified MPs are valid and will run on... |
| checkMSE | Utility functions for MSE objects |
| CheckOM | Check OM object is complete |
| ChkYrs | Check the years to summarize performance |
| Choose | Manually map parameters for the historical period of... |
| CombineMMP | Create a blank MP recommendations object (class Rec) of the... |
| Converge | Check Convergence |
| Cos_thresh_tab | Current default thresholds for COSEWIC satisficing |
| cparscheck | Internal function for checking that the 'OM@cpars' is... |
| Cplot | Plot the median biomass and yield relative to last historical... |
| CSRA | Catch at size reduction analysis |
| CSRAfunc | Optimization function for CSRA |
| cv | Calculate CV from vector of values |
| Data2csv | Converts a Data object into a .csv data file |
| Data-class | Class "Data" |
| Data-class-objects | Data class objects |
| DataDescription | DataDescription |
| DataDir | Directory of the data in the installed package on your... |
| DataInit | Initialize Data Input Files |
| DataSlots | DataSlots |
| Data_xl | Read in Data object from Excel spreadsheet |
| 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,... |
| DLMDataDir | Directory of the installed package on your computer |
| dnormal | Double-normal selectivity curve |
| Dom | Determine dominate MPs |
| expandHerm | Expand the Herm list in SexPars to a matrix of fractions at... |
| Fease | MP feasibility diagnostic |
| Fleet-class | Class "Fleet" |
| Fleet-class-objects | Fleet class objects |
| FleetDescription | FleetDescription |
| FMSYref | Reference management procedures |
| GenerateRandomWalk | Creates a time series per simulation that has a random normal... |
| genSizeCompWrap | Wrapper for C++ function to generate length composition |
| getAFC | Calculate age at first capture from length at first capture... |
| getBlow | Blow parallel optimization function |
| getclass | get object class |
| getDataList | Get part of an MP specific data-list |
| getEffhist | Calculate historical fishing mortality |
| getfirstlev | Extract the first dimension of a hierarchical list of... |
| getmov2 | Optimization function to find a movement model that matches... |
| getnIVs | Count independent variables for a MICE relationship at... |
| getq_multi_MICE | Optimize for catchability (q) and fishing dist for a MICE... |
| getsel | Calculate selectivity curve |
| hconv | Stock recruit parameterization |
| hist2 | Wrapper for histogram function |
| Hist-class | Class "Hist" |
| HistDescription | HistDescription |
| HistMICE | Reconstruct historical dynamics |
| hrate | Derives the rate of exchange from one sex to another based on... |
| Imp-class | Class "Imp" |
| Imp-class-objects | Imp class objects |
| ImpDescription | ImpDescription |
| initialize-methods | ~~ Methods for Function 'initialize' ~~ |
| Input | Function to run a set of input control methods |
| iSCAM | Reads iSCAM files into a hierarchical R list object |
| iSCAM2OM | Reads MPD or MCMC estimates and data from iSCAM file... |
| iSCAMcomps | Combines all iSCAM age composition data across fleets |
| iSCAMinds | Combines indices into a single index using linear modelling... |
| joinData | Join Data objects present in a list |
| join_plots | Plot several plots with a shared legend |
| Kplot | KOBE plot: a projection by projection plot of F/FMSY and... |
| L2A | Length to age conversion |
| label.class-class | Label class union for performance metric objects |
| Lag_Data | Lag the time-series slots in a 'Data' object by a specified... |
| ldim | Dimensions of a hierarchical list object |
| LH2OM | Predict missing life-history parameters |
| LHdatabase | LHdatabase |
| LinInterp | Linear interpolation of a y value at level xlev based on a... |
| makeMOM | Utility for making multi-OMs |
| makemov | Calculates movement matrices from user inputs for fraction in... |
| makeRel | MICE relationships for multi-OM |
| makeTransparent | Make colors transparent |
| ML2D | Depletion and F estimation from mean length of catches |
| MMSE-class | Class "MMSE" |
| MOM-class | Class "MOM" |
| MOM-class-objects | MOM class objects |
| movestockCPP | Apply the movement model to the stock for one time-step |
| movfit_Rcpp | Rcpp version of the Optimization function that returns the... |
| MPCalcsNAs | Fill any NAs arising from MPCalcs (hermaphroditism mode) |
| MPtype | Management Procedure Type |
| MPurl | Get help topic URL |
| MSE-class | Class "MSE" |
| MSEDescription | MSEDescription |
| MSEextra | Load more data from MSEextra package |
| MSYCalcs | Internal function to calculate MSY Reference Points |
| multiData | Combine data among fleets |
| multiDataS | Combine data among stocks |
| multidebug | A basic comparison of runMSE output (MSE) and multiMSE (MMSE) |
| multiMSE | Run a multi-fleet multi-stock Management Strategy Evaluation |
| NAor0 | Is a value NA or zero. |
| NIL | Item in list: get the list values from a list of lists |
| NOAA_plot | National Oceanographic and Atmospheric Administration default... |
| Obs-class | Class "Obs" |
| Obs-class-objects | Obs class objects |
| ObsDescription | ObsDescription |
| OM-class | Class "OM" |
| OM-class-objects | OM class objects |
| OMDescription | OMDescription |
| OMdoc | Generate OM Documentation Report |
| OMexample | Copy example OM XL and OM Documentation |
| OMinit | Initialize Operating Model |
| OneRep | Make stochastic variables certain for only one rep |
| optCPU | Determine optimal number of cpus |
| optMSY_eq | Internal wrapper function to calculate MSY reference points... |
| optQ | Optimize q for a single simulation |
| optYield | Optimize yield for a single simulation |
| PerformanceMetric | Performance Metrics Methods |
| plot.Data | Plot Data object |
| plotFun | Print out plotting functions |
| 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 |
| plotmulti | A basic SSB plot for debugging runMSE output |
| plotOFL | A generic OFL plot for NOAA use |
| plotquant | A fairly tidy time-series quantile plot |
| plotRel | Plot a relationship between stocks |
| plot.Stock | Plot Operating Model Object |
| PMLimit | Create a table of Performance Limits and Performance... |
| PMobj-class | An object for storing data for analysis using data-limited... |
| popdynCPP | Population dynamics model in CPP |
| popdynMICE | Population dynamics for a MICE model (multiyear) |
| popdynOneMICE | Population dynamics for a MICE model (single year) |
| popdynOneTScpp | Aging and Mortality for one time-step |
| 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... |
| prob.class-class | Prob class union for performance metric objects |
| PWhisker | Performance Whisker Plot |
| qestMICE | Internal function for optimizing catchability (q) for a MICE... |
| Range | Standardize values |
| RealFease | MP feasibility diagnostic using real data |
| Rec-class | Class "Rec" |
| Replace | Replace an existing Stock, Fleet, Obs, or Imp object |
| replic8 | Enlarge (replicate) a DLM data object to create an additional... |
| Report | Generate a Data Report |
| ReqData | ReqData |
| Required | What management procedures need what data |
| ResFromRel | Returns Results of a set of MICE relationships |
| runCOSEWIC | COSEWIC MSE run using the correct MPs and projected time... |
| runInMP | Runs input control MPs on a Data object. |
| runMP | Run a Management Procedure |
| runMSE | Run a Management Strategy Evaluation |
| SampleCpars | Sample custom pars |
| SampleFleetPars | Sample Fleet Parameters |
| SampleImpPars | Sample Implementation Error Parameters |
| SampleObsPars | Sample Observation Parameters |
| sample_steepness2 | Sample steepness given mean and cv |
| SampleStockPars | Sample Stock parameters |
| sdconv | Get parameters of lognormal distribution from mean and... |
| Sense | Sensitivity analysis |
| setup | Setup parallel processing |
| show-MSE | Show the output of a PM |
| show-MSEtool | Show MSEtool S4 objects |
| show-Rec | Show the output of a single MP recommendation |
| SIL | Slot in list: get the slot values from a list of objects |
| simCAA | Simulate Catch-at-Age Data |
| simCAL | Simulate Catch-at-Length Data |
| simmov | Calculates movement matrices from user inputs |
| SimulatedData | SimulatedData Data |
| SketchFun | Manually map the historical relative fishing effort... |
| SS2Data | Reads data Stock Synthesis file structure into a Data object... |
| SS2DataMOM | Reads data Stock Synthesis file structure into a nested Data... |
| SS2MOM | Import Stock Synthesis to MOM (2-sex multi-fleet) or OM... |
| SSBrefplot | Plot Spawning stock biomass and reference points for both... |
| Stock-class | Class "Stock" |
| Stock-class-objects | Stock class objects |
| 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 |
| summary-Data | Summary of Data object |
| summary-MMSE | Summary of MMSE object |
| summary-MSE | Summary of MSE object |
| TAC | Calculate TAC recommendations for more than one MP |
| TACfilter | TAC Filter |
| Taxa_Table | Taxa_Table |
| TEG | Tom's expand grid |
| Thresh_tab | Current default thresholds for DFO satisficing |
| tinyErr | Remove observation, implementation, and process error |
| TradePlot | Generic Trade-Plot Function |
| trlnorm | Lognormal distribution |
| Turing | Turing Test |
| Uses | Find the Management Procedures that use a particular data... |
| validcpars | Valid custom parameters (cpars) |
| 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... |
| wormplot | Biomass wormplot |
| writeCSV | Internal function to write CSVs for objects |
| 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 |
