| Access and Assign Slots from Compatible S4 Objects | AC AC<- Access Beta Beta<- Bias Bias<- Classes Classes<- Compliance Compliance<- CPUE CPUE<- CV CV<- CVatAge CVatAge<- DiscardsAtAge DiscardsAtAge<- DiscardsAtSize DiscardsAtSize<- Dist Dist<- Error Error<- Exploitation Exploitation<- LandingsAtAge LandingsAtAge<- LandingsAtSize LandingsAtSize<- LifeHistory LifeHistory<- Mean Mean<- MeanAtAge MeanAtAge<- MeanAtLength MeanAtLength<- MeanAtWeight MeanAtWeight<- Misc Misc<- Model Model<- nAge Name Name<- nArea nComplex nFleet nSim nSim<- nStock Pars Pars<- Period Period<- Random Ref Ref<- RefCV RefCV<- Reference Reference<- SD SD<- Size Size<- Survey Survey<- Timing TruncSD TruncSD<- Units Units<- Value Value<- YearLH YearLH<- |
| Add Auto-Correlation to a Vector of Values | AddAutoCorrelation |
| Add a Fleet to an Operating Model | AddFleet |
| Utility functions for multiMSE objects | addMMPs |
| Management Advice Constructor and Accessors | Advice |
| The 'advice' S4 Class | advice-class |
| The 'advicedata' S4 Class | AdviceData advicedata advicedata-class |
| Ages Constructor and Accessors | Ages Ages<- MaxAge MaxAge<- MinAge MinAge<- PlusGroup PlusGroup<- |
| The 'ages' S4 Class | ages-class |
| Age-Structured Observation Model | AgeStructuredObs |
| Stock class objects | Albacore Bluefin_tuna Bluefin_tuna_WAtl Blue_shark Butterfish Herring Mackerel Porgy Rockfish Snapper Sole Stock-class-objects Toothfish |
| MOM class objects | Albacore_TwoFleet MOM-class-objects |
| Albacore Example Stock | AlbacoreExStock |
| Apply AR(1) autocorrelation to residuals, skipping NAs | ApplyAC |
| Apply multi Management Procedures (class MMP) to a hierarchical list of Data class objects | applyMMP |
| Apply Management Procedures to an object of class Data | applyMP |
| Convert Between Arrays and Data Frames | Array2DF array_df_conversion DF2Array |
| Perform Operations on Two Arrays | ArrayDivide ArrayExtend ArrayFill<- ArrayMultiply ArrayOperations ArraySubtract ArraySum |
| Convert ASAP 3 assessments into an operating model | ASAP2Data ASAP2OM |
| Reads bootstrap estimates from a stock assessment model into a multi-fleet operating model. | Assess2MOM |
| Reads bootstrap estimates from a stock assessment model (including VPA) into an operating model. 'Assess2OM' is identical to 'VPA2OM'. | Assess2OM VPA2OM |
| Asymptotic Selectivity Example Fleet | AsympExFleet |
| Data class objects | Atlantic_mackerel China_rockfish Cobia Data-class-objects Example_datafile Gulf_blue_tilefish ourReefFish Red_snapper Simulation_1 |
| What objects of this class are available | avail |
| Reads MCMC estimates from Awatea (Paul Starr) processed r file structure into an operating model | Awatea2OM |
| Import a multi-stock, multi-fleet OM from a BAM object | BAM2MOM BAM2OM |
| Get and Fix BAM Fleet Names | BAMFleetNames FixFleetNames GetBAMFleetNames |
| Extract Biological Time Series | Biomass bio_timeseries SBiomass SProduction |
| Bioeconomic | Bioeconomic Bioeconomic<- Cost Cost<- Depreciation Depreciation<- Discount Discount<- Disinvestment Disinvestment<- Investment Investment<- Revenue Revenue<- |
| The 'bioeconomic' S4 Class | bioeconomic-class |
| Boxplot of TAC recommendations | boxplot.Data |
| Butterfish Example Stock | ButterfishExStock |
| Calculate Age Classes | CalcAgeClasses |
| Calculate an Age-Size Key | CalcAgeSizeKey |
| Calculate the Asymptotic Spatial Distribution of a Movement Matrix | CalcAsymDist |
| Calculate Absolute Equilibrium Quantities | CalcEquilibrium |
| Calculate Innovation Covariance Matrix for Multivariate AR(1) | CalcInnovationCov |
| Calculate MSY Reference Points | CalcMSY |
| Calculate Per-Recruit Quantities | CalcPerRecruit |
| Calculate Reference Yield | calcRefYield |
| Calculate residual statistics for log-space index residuals | CalcResidualStats |
| Unfished Spawning Production Per Recruit | CalcSPR0 |
| Calculate Cumulative Survival-at-Age | CalcSurvival |
| Convert Between Season Count and Time Unit Labels | CalcSeasons CalcTSUnits |
| Calculate Dynamic Unfished Population Dynamics | CalcUnfished_Dynamic |
| Calculate Equilibrium Unfished Population Dynamics | CalcUnfished_Equilibrium |
| Calculate the Unfished Spatial Distribution | CalcUnfishedDist |
| Calculate Equilibrium Unfished Number-at-Age | CalcUnfishedNumber |
| Calculate Unfished Survival | CalcUnfishedSurvival |
| Simplifies the CAL slot of data object | CALsimp |
| Identify management procedures (MPs) based on data availability | Can Cant DLMdiag Needed |
| Extract or Assign Catch Time Series | catch_timeseries Discards Discards<- Interactions Landings Landings<- Removals |
| Catchability Constructor and Accessors | Catchability Catchability<- Efficiency Efficiency<- qCV qCV<- qInc qInc<- Theta Theta<- |
| The 'catchability' S4 Class | catchability-class |
| Catch-and-Survey Observation Model | CatchAndSurveyObs |
| CatchData Constructor | CatchData |
| The 'catchdata' S4 Class | catchdata-class |
| CatchObs Constructor and Accessors | CatchObs |
| The 'catchobs' S4 Class | catchobs-class |
| Check catch data availability and units | CheckCatch |
| Check for duplicated MPs names | CheckDuplicate |
| Check that specified MPs are valid and will run on MSEtool::SimulatedData | CheckMPs |
| Utility functions for MSE objects | addMPs checkMSE joinHist joinMSE updateMSE |
| Check OM object is complete | CheckOM |
| Check that a required package is installed | CheckPackage |
| Manually map parameters for the historical period of operating model | Choose ChooseEffort ChooseM ChooseSelect |
| Combine Multiple Fleets into a Single Fleet | CombineFleets |
| Create a blank MP recommendations object (class Rec) of the right dimensions | CombineMMP |
| Combine Multiple Operating Models into One | CombineOMs |
| Commercial-Fleet Observation Model | CommercialFleetObs |
| Compare BAM and OM Output | CompareBAM |
| Compare SS3 and OM fishery dynamics | CompareSS CompareSS_Biomass CompareSS_Number |
| CompData Constructor | CompData |
| The 'compdata' S4 Class | compdata-class |
| Stock Complex Example Operating Model | ComplexOM |
| CompObs Constructor and Accessors | CompObs |
| The 'compobs' S4 Class | CompObs-class compobs-class |
| Default OM Control Options | ControlDefault |
| Check Convergence | Converge |
| Convert legacy S4 objects to new S4 object classes | Convert |
| Convert a Legacy Data Object to a New data Class | ConvertData |
| Convert a Legacy Fleet Object to the Current 'fleet' Class | ConvertFleet |
| Convert a Legacy Imp Object to a New imp Class | ConvertImp |
| Convert Legacy MOM Object to New om Class | ConvertMOM |
| Convert a Legacy Obs Object to the Current 'obs' Class | ConvertObs |
| Convert Legacy OM Object to New om Class | ConvertOM |
| Convert a Legacy Stock Object to the Current 'stock' Class | ConvertStock |
| Current default thresholds for COSEWIC satisficing | Cos_thresh_tab |
| Internal function for checking that the 'OM@cpars' is formatted correctly | cparscheck |
| Plot the median biomass and yield relative to last historical year | Cplot |
| Convert Between Steepness and Compensation Ratio | CR2h h2CR |
| Constructor and Accessor for 'Data' | Data |
| Read in Data object from Excel spreadsheet | Data_xl |
| The 'data' S4 Class | data-class |
| Class ''Data'' | Data-class Data-legacy-class |
| Converts a Data object into a .csv data file | Data2csv |
| DataDescription | DataDescription |
| Directory of the data in the installed package on your computer | DataDir |
| Data Helper Functions | DataHelpers LastHistYearInd LastTAC ProjectionYear |
| Initialize Data Input Files | DataInit |
| Data-Rich Observation Model | DataRichObs |
| DataSlots | DataSlots |
| Trim Data Object by Final Year | DataTrim |
| Fleet class objects | DecE_Dom DecE_HDom DecE_NDom FlatE_Dom FlatE_HDom FlatE_NDom Fleet-class-objects Generic_DecE Generic_FlatE Generic_Fleet Generic_IncE IncE_HDom IncE_NDom Low_Effort_Non_Target Targeting_Small_Fish Target_All_Fish |
| Default Ages and Years | DefaultAges DefaultYears |
| Delete the Log Directory | DeleteLogs |
| Depletion Constructor and Accessors | Depletion Depletion<- Final Final<- Initial Initial<- |
| The 'depletion' S4 Class | depletion-class |
| Department of Fisheries and Oceans stock status bar plot | DFO_bar |
| Department of Fisheries and Oceans historical plot | DFO_hist |
| Department of Fisheries and Oceans trade-off plot | DFO_plot |
| Department of Fisheries and Oceans default plot 2 | DFO_plot2 |
| Department of Fisheries and Oceans projection plot | DFO_proj |
| Department of Fisheries and Oceans biomass quantile plot | DFO_quant |
| Create a standard DFO MSE report | DFO_report |
| DFO performance spider plot (top three MPs) | DFO_spider |
| Create a standard DFO performance table | DFO_tab |
| A formatted version of the standard DFO performance plot, color coded by thresholds | DFO_tab_formatted |
| Dimensions of an Object | dim |
| Add or Drop Named Dimensions of an Array | AddDimension dimension-utils DropDimension |
| Discard Mortality | DiscardMortality DiscardMortality<- |
| The 'discardmortality' S4 Class | discardmortality-class |
| Directory of the installed package on your computer | DLMDataDir |
| Hockey Stick Harvest control rule that modifies TAC. | doHCR |
| Create indices that are sampled at various frequencies | doIfreq |
| Determine dominate MPs | Dom |
| Dome-Shaped Selectivity Example Fleet | DomeExFleet |
| Calculate a management recommendation given constraints | doRec |
| Effort Constructor and Accessors | AnglerPerTrip AnglerPerTrip<- Distribution Distribution<- Effort Effort<- Maximum Maximum<- Mode Mode<- Targeting Targeting<- TripsScalar TripsScalar<- |
| The 'effort' S4 Class | effort-class |
| EffortData Constructor and Accessors | EffortData |
| The 'effortdata' S4 Class | effortdata-class |
| EffortObs Constructor and Accessors | EffortObs |
| The 'effortobs' S4 Class | effortobs-class |
| A flexible empirical management procedure. | Emp |
| Test Whether an Object is Empty | EmptyObject |
| The 'equilibrium' S4 Class | equilibrium-class |
| Example Management Procedures | AverageCatch CurrentCatch CurrentEffort CurrentLandings ExampleMPs |
| 'exploitationdata' Class | ExploitationData exploitationdata-class |
| ExploitationObs Constructor | ExploitationObs |
| The 'exploitationobs' S4 Class | exploitationobs-class |
| Extend an Array Along Named Dimensions | Extend ExtendAges ExtendAreas ExtendClasses ExtendSims ExtendYears |
| Unfished Reference Point Quantities | B0 extract-unfished N0 SB0 SP0 |
| MP feasibility diagnostic | Fease |
| Fecundity Constructor and Accessors | Fecundity Fecundity<- |
| The 'fecundity' S4 Class | fecundity-class |
| Fecundity Models | Fecundity-Models FecundityAtAge FecundityAtLength FecundityAtWeight FecundityModels FecundityModelsAge FecundityModelsLength FecundityModelsWeight |
| Extract Fishing Mortality Time Series | FDead FInteract FRetain F_timeseries |
| Fit a Movement Matrix to Target Spatial Parameters | FitMovement |
| Fit statistical properties of historical stock targeting | FitStockTargeting |
| Fleet | Closure Closure<- Fleet Fleet<- WeightFleet WeightFleet<- |
| The 'fleet' S4 Class | fleet-class |
| Class ''Fleet'' | Fleet-class Fleet-legacy-class |
| FleetDescription | FleetDescription |
| Reference management procedures | curEref FMSYref FMSYref50 FMSYref75 NFref |
| Generate Stochastic Stock Targeting Trajectories | GenerateStockTargeting |
| Obs class objects | Generic_Obs Imprecise_Biased Imprecise_Unbiased Obs-class-objects Perfect_Info Precise_Biased Precise_Unbiased |
| Generate Stochastic Historical Effort Time Series | GenHistEffort |
| Generate Mean-at-Age, Length, or Weight Arrays | GenMeanAtAge GenMeanAtLength GenMeanAtWeight |
| Generate Correlated Multi-Stock Recruitment Deviations | GenMultiStockRecDevs |
| Generate Stock-Recruitment Deviations | GenRecDevs |
| Generate (log-space) residuals with truncated log-normal distribution | GenResiduals |
| get object class | getclass |
| Get part of an MP specific data-list | getDataList |
| Extract the first dimension of a hierarchical list of recommendation objects | getfirstlev |
| Retrieve Operating Model Metadata | GetMetaData |
| Optimization function to find a movement model that matches user specified movement characteristics modified for Rcpp. | getmov2 |
| Search R session for MP | getMP |
| Count independent variables for a MICE relationship at position x in a Rel list | getnIVs |
| Calculate selectivity curve | getsel |
| Get Reference Points from Stock Synthesis Output | GetSSRefPoints |
| Stock recruit parameterization | hconv R0conv SRalphaconv SRbetaconv |
| Internal Herm functions | checkHerm expandHerm Herm-int subsetHerm |
| 'hist' Class and Accessor | Hist |
| 'hist' Class | hist-class |
| Class ''Hist'' | Hist-class Hist-legacy-class |
| Wrapper for histogram function | hist2 |
| HistDescription | HistDescription |
| Imp Constructor and Accessor | Imp |
| Implementation Error | imp-class |
| Class ''Imp'' | Imp-class Imp-legacy-class |
| ImpDescription | ImpDescription |
| Import BAM Output into an Operating Model | GetBAMOutput ImportBAM ListBAMStocks |
| Import BAM Assessment Data into an Operating Model | ImportBAMData |
| Import a Stock Synthesis Model into an Operating Model | ImportSS |
| Import SS3 data into a Data object | ImportSSData |
| Import SS3 Report directories with optional parallel processing | ImportSSReport |
| ImpSlot Constructor and Accessors | ImpSlot |
| The 'indicesdata' S4 Class | indicesdata-class |
| IndicesObs Constructor and Accessors | IndicesObs |
| The 'indicesobs' S4 Class | indicesobs-class |
| ~~ Methods for Function 'initialize' ~~ | initialize-methods |
| Function to run a set of input control methods | Input |
| Reads iSCAM files into a hierarchical R list object | fetch.file.names iSCAM load.iscam.files read.control.file read.data.file read.mcmc read.par.file read.projection.file read.report.file |
| Reads MPD or MCMC estimates and data from iSCAM file structure into an operating model | iSCAM2Data iSCAM2OM |
| Combines all iSCAM age composition data across fleets | iSCAMcomps |
| Combines indices into a single index using linear modelling (** Deprecated **) | iSCAMinds |
| Test Whether an Object is a Default-Constructed Instance | isNewObject |
| Plot several plots with a shared legend | join_plots |
| Join Data objects present in a list | joinData |
| Join Two Objects Along the Year Dimension | JoinYear |
| KOBE plot: a projection by projection plot of F/FMSY and B/BMSY | Kplot |
| Lag the time-series slots in a 'Data' object by a specified number of time-steps | Lag_Data |
| Dimensions of a hierarchical list object | ldim |
| Length Constructor and Accessors | ALK ALK<- Length Length<- |
| Length-at-Age Growth Models | Brody Gompertz Length-at-Age-Models LengthModels Schnute vonBert |
| The 'length' S4 Class | length-class |
| Length-Structured Observation Model | LengthStructuredObs |
| Predict missing life-history parameters | LH2OM predictLH |
| LHdatabase | LHdatabase |
| 'lifehistorydata' Class | LifeHistoryData lifehistorydata-class |
| LifeHistoryObs Constructor | LifeHistoryObs |
| The 'lifehistoryobs' S4 Class | lifehistoryobs-class |
| Convert Between Lists and Arrays | Array2List list-array-conversion List2Array |
| Load Function Arguments into an Environment | LoadArgs |
| Display Log Warnings | Log |
| Logit and Inverse Logit (Sigmoid) Functions | ilogit logit |
| Utility for making multi-OMs | makeMOM |
| Calculates movement matrices from user inputs for fraction in each area (fracs) and probability of staying in areas (prob) | makemov |
| 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. | makemov2 |
| MICE relationships for multi-OM | makeRel predict.Rel print.Rel simulate.Rel |
| Make colors transparent | makeTransparent |
| Maturity Constructor and Accessors | Maturity Maturity<- Semelparous Semelparous<- |
| The 'maturity' S4 Class | maturity-class |
| Maturity Models: Age, Length, and Weight | Maturity-Models MaturityAtAge MaturityAtLength MaturityAtWeight MaturityModels MaturityModelsAge MaturityModelsLength MaturityModelsWeight |
| Depletion and F estimation from mean length of catches | ML2D |
| Class ''MMSE'' | MMSE-class MMSE-legacy-class |
| Selectivity, Retention, Weight, Fecundity, and Maturity Model Helpers | allometric dnormal double_normal logistic_50_95 model-helpers |
| Class ''MOM'' | MOM-class MOM-legacy-class |
| Apply the movement model to the stock for one time-step | movestockCPP |
| Rcpp version of the Optimization function that returns the squared difference between user specified and calculated movement parameters. | movfit_Rcpp |
| Fill any NAs arising from MPCalcs (hermaphroditism mode) | MPCalcsNAs |
| Management Procedure Type | MPtype |
| 'mse' Class | mse-class |
| Class ''MSE'' | MSE-class MSE-legacy-class |
| Convert an 'mse' Object to a Slick Object | MSE2Slick |
| MSEDescription | MSEDescription |
| Load more data from MSEextra package | MSEextra |
| Access MSY Reference Point Slots | BMSY FMSY MSY-accessors MSYDiscards MSYLandings MSYRefs SBMSY SPMSY SPRMSY |
| Internal function to calculate MSY Reference Points | MSYCalcs |
| Combine data among fleets | multiData |
| Combine data among stocks | multiDataS |
| A basic comparison of runMSE output (MSE) and multiMSE (MMSE) | multidebug |
| Multi-Stock Multi-Fleet Example Operating Model | MultiStockOM |
| Access Stock or Fleet Names | FleetNames name-accessors StockNames |
| NaturalMortality Constructor and Accessors | NaturalMortality NaturalMortality<- |
| The 'naturalmortality' S4 Class | naturalmortality-class |
| Natural Mortality Models | LorenzenMortalityLength LorenzenMortalityWeight MortalityAtAge NaturalMortality-Models NaturalMortalityModels |
| Item in list: get the list values from a list of lists | NIL |
| National Oceanographic and Atmospheric Administration default plot 1 | NOAA_plot |
| Extract Number-at-Age time series | Number |
| Obs Constructor and Accessor | Obs Obs<- |
| The 'obs' S4 Class | obs-class |
| Class ''Obs'' | Obs-class Obs-legacy-class |
| ObsDescription | ObsDescription |
| OM Constructor and Accessor | OM |
| Access and Modify OM Slots | Agency Agency<- Allocation Allocation<- Author Author<- CatchFrac CatchFrac<- Complexes Complexes<- Control Control<- CurrentYear CurrentYear<- DataLag DataLag<- EFactor EFactor<- Email Email<- Herm Herm<- Interval Interval<- Latitude Latitude<- Longitude Longitude<- maxF maxF<- nReps nReps<- nYear nYear<- OM-accessors pStar pStar<- pYear pYear<- Region Region<- Relations Relations<- Seasons Seasons<- Seed Seed<- SharePar SharePar<- Source Source<- Sponsor Sponsor<- |
| The 'om' S4 Class | om-class |
| Class ''OM'' | OM-class OM-legacy-class |
| OMDescription | OMDescription |
| Generate OM Documentation Report | OMdoc |
| Copy example OM XL and OM Documentation | OMexample |
| Initialize Operating Model | OMinit |
| Determine optimal number of cpus | optCPU |
| Imp class objects | Imp-class-objects Overages Perfect_Imp |
| Performance Metrics Methods | AAVE AAVY LTY P10 P100 P50 PerformanceMetric PGK PNOF STY Yield |
| The 'perrecruit' S4 Class | perrecruit-class |
| Plot Data object | plot.Data |
| Standard plot for an object of class MMSE (multi MSE) | plot.MMSE |
| Standard plot for an object of class MOM | plot,MOM,missing-method plot.MOM |
| Plot MSE object | plot.MSE |
| Plot Operating Model Object | plot.Fleet plot.Hist plot.Imp plot.Obs plot.OM plot.pars plot.Stock |
| Print out plotting functions | plotFun |
| A basic SSB plot for debugging runMSE output | plotmulti |
| A generic OFL plot for NOAA use | plotOFL |
| A fairly tidy time-series quantile plot | plotquant |
| Plot a relationship between stocks | plotRel |
| Create a table of Performance Limits and Performance Objectives | PMLimit PMObj |
| An object for storing data for analysis using data-limited methods | PMobj-class |
| 'popdynamics' Class | popdynamics popdynamics-class |
| Populate Operating Model Components | Populate |
| Populate a Catchability Object | PopulateCatchability |
| Populate Catch Observation Error | PopulateCatchObs |
| Populate a Closure Object | PopulateClosure |
| Populate Composition Observation Error | PopulateCompObs |
| Populate a Depletion Object | PopulateDepletion |
| Populate a DiscardMortality Object | PopulateDiscardMortality |
| Populate an Effort Object | PopulateEffort |
| Populate Effort Observation Error | PopulateEffortObs |
| Populate a Fecundity Object | PopulateFecundity |
| Populate a Fleet Object | PopulateFleet |
| Populate Index Observation Error | PopulateIndexObs |
| Populate a Length Object | PopulateLength |
| Populate a Maturity Object | PopulateMaturity |
| Populate a Natural Mortality Object | PopulateNaturalMortality |
| Populate an Obs Object | PopulateObs |
| Populate an Operating Model | PopulateOM |
| Populate a Retention Object | PopulateRetention |
| Populate a Selectivity Object | PopulateSelectivity |
| Populate a Spatial Object | PopulateSpatial |
| Populate an SRR Object | PopulateSRR |
| Populate a Stock Object | PopulateStock |
| Populate a Weight-at-Age Object | PopulateWeight |
| Specifying Biological and Fleet Schedules | pars-model-meanatage populating-schedules schedule-population |
| Extract and Reconstruct Posterior Predicted Data (PPD) | PPD |
| A projection by projection plot of F/FMSY and B/BMSY | Pplot |
| A projection by projection plot of F/FMSY, B/BMSY, B/B0, and yield | Pplot2 |
| Print method for 'multiHist' objects | print.multiHist |
| Print a 'RepList' object | print.RepList |
| Project an Operating Model Over the Projection Period | Project |
| Performance Whisker Plot | PWhisker |
| A quantile plot | quantile_plot |
| Dirichlet-Multinomial Sampler | rDirichletMultinomial |
| MP feasibility diagnostic using real data | RealFease |
| Class ''Rec'' | Rec-class |
| Reduce redundant Sim, Year, and Age dimensions in arrays | ReduceDims |
| Reduce the number of simulations | ReduceNSim |
| Reference Points Object | reference-class |
| 'referencedata' Class | ReferenceData referencedata-class |
| The 'refpointsMSY' S4 Class | refpointsMSY-class |
| Rename Stocks and Fleets in an OM | Rename |
| Reorder Stocks and Fleets in an OM | Reorder |
| Replace an existing Stock, Fleet, Obs, or Imp object | Replace |
| Enlarge (replicate) a DLM data object to create an additional dimension for simulation / sensitivity testing | replic8 |
| Generate a Data Report | Report |
| ReqData | ReqData |
| What management procedures need what data | Required |
| Retention | Retention Retention<- |
| The 'retention' S4 Class | retention-class |
| Retention Models | DoubleNormalRetention DoubleNormalRetentionWeight Retention-Models RetentionAtAge RetentionAtLength RetentionAtWeight RetentionKnifeEdgeAge RetentionKnifeEdgeLength RetentionModels RetentionModelsAge RetentionModelsLength RetentionModelsWeight |
| COSEWIC MSE run using the correct MPs and projected time horizon | COSEWIC_Blow COSEWIC_Dplot COSEWIC_Hplot COSEWIC_Pplot COSEWIC_report COSEWIC_tab COSEWIC_tab_formatted runCOSEWIC |
| Runs input control MPs on a Data object. | runInMP |
| Run a Management Procedure | runMP |
| Run a Management Strategy Evaluation | runMSE |
| Summarise S4 Object Memory Usage by Slot | S4SlotSizes |
| Save an Object to Disk | Save |
| Select DataList for an MP from 'MMSE@PPD' | select_MP |
| Selectivity | isRel isRel<- Selectivity Selectivity<- |
| The 'selectivity' S4 Class | selectivity-class |
| Selectivity Models | DoubleNormal DoubleNormalWeight Selectivity-Models SelectivityAtAge SelectivityAtLength SelectivityAtWeight SelectivityKnifeEdgeAge SelectivityKnifeEdgeLength SelectivityModels SelectivityModelsAge SelectivityModelsLength SelectivityModelsWeight |
| Sensitivity analysis | Sense |
| Setup parallel processing | setup |
| Set Up Parallel Processing for openMSE Workflows | CheckParallel DisableParallel SetupParallel |
| Show Methods | show,advice-method show,ages-method show,catchability-method show,catchobs-method show,compobs-method show,data-method show,depletion-method show,discardmortality-method show,effort-method show,effortobs-method show,equilibrium-method show,exploitationobs-method show,fecundity-method show,fleet-method show,hist-method show,indicesobs-method show,length-method show,lifehistoryobs-method show,maturity-method show,mse-method show,naturalmortality-method show,obs-method show,om-method show,perrecruit-method show,popdynamics-method show,refpointsMSY-method show,retention-method show,selectivity-method show,spatial-method show,srr-method show,stock-method show,stocktargeting-method show,weight-method show-methods |
| Show MSEtool S4 objects | show show,Data-method show,Hist-method show,MMSE-method show,MOM-method show,MSE-method show,OM-method show-MSEtool |
| Show the output of a PM | show,PMobj-method |
| Show the output of a single MP recommendation | show,Rec-method |
| Slot in list: get the slot values from a list of objects | SIL |
| Simulate Catch-at-Age Data | simCAA |
| Simulate Catch-at-Length Data | simCAL |
| Calculates movement matrices from user inputs | plot_mov simmov |
| Calculates movement matrices from user specified distribution among other areas | simmov2 |
| Simulate Operating Model Dynamics | Simulate |
| SimulatedData Data | SimulatedData |
| Run a multi-fleet multi-stock Management Strategy Evaluation | multiMSE ProjectMOM SimulateMOM |
| Single Stock Example Operating Model | SingleStockOM |
| Manually map the historical relative fishing effort trajectory. | SketchFun |
| General purpose polynomial smoother | smoothy |
| Spatial Constructor and Accessors | Arrangement Arrangement<- CVDist CVDist<- CVStay CVStay<- FracOther FracOther<- Movement Movement<- ProbStaying ProbStaying<- RelativeSize RelativeSize<- Spatial Spatial<- UnfishedDist UnfishedDist<- |
| The 'spatial' S4 Class | spatial-class |
| Standard MSE projection plot | Splot |
| SRR Constructor and Accessors | R0 R0<- RecDevHist RecDevHist<- RecDevInit RecDevInit<- RecDevProj RecDevProj<- RelRecFun RelRecFun<- SpawnTimeFrac SpawnTimeFrac<- SPFrom SPFrom<- SRR SRR<- |
| The 'srr' S4 Class | srr-class |
| Stock–Recruitment Relationships (SRR) | BevertonHolt BevertonHolt_RelRec HockeyStick HockeyStick_RelRec Ricker Ricker_RelRec SRRModels |
| Reads data Stock Synthesis file structure into a Data object using package r4ss | SS2Data |
| Reads data Stock Synthesis file structure into a nested Data object analogous with multiMSE | SS2DataMOM |
| Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet) | MOM_agg_fleets plot_SS2MOM plot_SS2OM SS2MOM SS2OM SSMOM2OM |
| Plot Spawning stock biomass and reference points for both historical and projected period | SSBrefplot |
| Standardize fishing effort across stocks for each fleet | StandardizeEffort |
| Stock Constructor and Accessors | CommonName CommonName<- Species Species<- Stock Stock<- |
| The 'stock' S4 Class | stock-class |
| Class ''Stock'' | Stock-class Stock-legacy-class |
| StockDescription | StockDescription |
| Stock Targeting Constructor | StockTargeting |
| The 'stocktargeting' S4 Class | stocktargeting-class |
| Subset MSE object by management procedure (MP) or simulation. | Sub |
| Subset the cpars slot in an operating model | SubCpars SubCpars,MOM-method SubCpars,OM-method |
| Subset a Stock, Fleet, Obs, or Imp object from an OM object | SubOM |
| Subset an object by simulation, year, age, MP, and/or fleet | Subset |
| Summary of Data object | summary,Data-method |
| Summary of MMSE object | summary,MMSE-method |
| Summary of MSE object | summary,MSE-method |
| Sum over named array dimensions | SumOverAge SumOverArea SumOverClass SumOverFleet SumOverStock SumOverYear |
| Calculate TAC recommendations for more than one MP | TAC |
| TAC Filter | TACfilter |
| Extract TAC Recommendations from an MSE Object | TACs |
| Taxa_Table | Taxa_Table |
| Tom's expand grid | TEG |
| OM class objects | OM-class-objects testOM |
| Current default thresholds for DFO satisficing | Thresh_tab |
| 'Timeseries' Class | timeseries-class |
| Remove observation, implementation, and process error | tinyErr tinyErr,OM-method |
| Generic Trade-Plot Function | NOAA_plot2 Tplot Tplot2 Tplot3 TradePlot |
| Tune MP | tune_MP |
| Turing Test | Turing TuringMOM |
| Two-Fleet Example Operating Model | TwoFleetOM |
| 'unfished' Class | Dynamic Equilibrium Unfished unfished unfished-class |
| Unit Conversion Functions | inch2mm kg2lb kg2mt kg2_1000lb lb2kg lb2mt mm2inch unit-conversions |
| Update an S4 Object and Its Slots | UpdateObject UpdateSlots |
| Find the Management Procedures that use a particular data slot | Uses |
| Valid custom parameters (cpars) | validcpars |
| Return Valid Units | ValidUnits |
| Calculate Value Of Information | VOI |
| Calculate Value Of Information 2 | VOI2 |
| Yet another Value of Information Plot | VOIplot |
| Weight Constructor and Accessors | AWK AWK<- Weight Weight<- |
| The 'weight' S4 Class | weight-class |
| Weight-at-Age and Weight-at-Length Models | Weight-Models WeightatAge WeightatLength WeightatMeanLength WeightModels |
| Takes a fitted SAM model and samples historical population and fishing dynamics from the MLE fit and variance-covariance matrix. | WHAM2OM |
| Biomass wormplot | wormplot |
| Wrapped Normal Distribution | WrappedNormal |
| Internal function to write CSVs for objects | writeCSV |
| Import a Data object from Excel file | XL2Data |
| Import Fleet Object from Excel file | XL2Fleet |
| Load OM from Excel file | XL2OM |
| Import Stock Object from Excel file | XL2Stock |
| Calculate or Extract Time Step Values | CalcYears Years |
