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"SimulatedData Data", "object": "SimulatedData", "class": [ "Data" ], "fields": [], "table": false, "tojson": false }, { "name": "Simulation_1", "title": "Data class objects", "object": "Simulation_1", "class": [ "Data" ], "fields": [], "table": false, "tojson": false }, { "name": "SingleStockOM", "title": "Single Stock Example Operating Model", "object": "SingleStockOM", "class": [ "om" ], "fields": [], "table": false, "tojson": false }, { "name": "Snapper", "title": "Stock class objects", "object": "Snapper", "class": [ "Stock" ], "fields": [], "table": false, "tojson": false }, { "name": "Sole", "title": "Stock class objects", "object": "Sole", "class": [ "Stock" ], "fields": [], "table": false, "tojson": false }, { "name": "StockDescription", "title": "StockDescription", "object": "StockDescription", "class": [ "data.frame" ], "fields": [ "Slot", "Description" ], "rows": 27, "table": true, "tojson": true }, { "name": "Target_All_Fish", "title": "Fleet class objects", "object": "Target_All_Fish", "class": [ "Fleet" ], "fields": [], "table": false, "tojson": false }, { "name": "Targeting_Small_Fish", "title": "Fleet class objects", "object": "Targeting_Small_Fish", "class": [ "Fleet" ], "fields": [], "table": false, "tojson": false }, { "name": "Taxa_Table", "title": "Taxa_Table", "object": "Taxa_Table", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "SpecCode", "Species", "Genus", "Subfamily", "Family", "Order", "Class", "SuperClass" ], "rows": 34721, "table": true, "tojson": true }, { "name": "testOM", "title": "OM class objects", "object": "testOM", "class": [ "OM" ], "fields": [], "table": false, "tojson": false }, { "name": "Toothfish", "title": "Stock class objects", "object": "Toothfish", "class": [ "Stock" ], "fields": [], "table": false, "tojson": false }, { "name": "TwoFleetOM", "title": "Two-Fleet Example Operating Model", "object": "TwoFleetOM", "class": [ "om" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "Access", "title": "Access and Assign Slots from Compatible S4 Objects", "topics": [ "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<-" ] }, { "page": "AddAutoCorrelation", "title": "Add Auto-Correlation to a Vector of Values", "topics": [ "AddAutoCorrelation" ] }, { "page": "AddFleet", "title": "Add a Fleet to an Operating Model", "topics": [ "AddFleet" ] }, { "page": "addMMPs", "title": "Utility functions for multiMSE objects", "topics": [ "addMMPs" ] }, { "page": "Advice", "title": "Management Advice Constructor and Accessors", "topics": [ "Advice" ] }, { "page": "advice-class", "title": "The 'advice' S4 Class", "topics": [ "advice-class" ] }, { "page": "advicedata-class", "title": "The 'advicedata' S4 Class", "topics": [ "AdviceData", "advicedata", "advicedata-class" ] }, { "page": "Ages", "title": "Ages Constructor and Accessors", "concept": [ "ages" ], "topics": [ "Ages", "Ages<-", "MaxAge", "MaxAge<-", "MinAge", "MinAge<-", "PlusGroup", "PlusGroup<-" ] }, { "page": "ages-class", "title": "The 'ages' S4 Class", "concept": [ "ages" ], "topics": [ "ages-class" ] }, { "page": "AgeStructuredObs", "title": "Age-Structured Observation Model", "concept": [ "obs-examples" ], "topics": [ "AgeStructuredObs" ] }, { "page": "Stock-class-objects", "title": "Stock class objects", "topics": [ "Albacore", "Bluefin_tuna", "Bluefin_tuna_WAtl", "Blue_shark", "Butterfish", "Herring", "Mackerel", "Porgy", "Rockfish", "Snapper", "Sole", "Stock-class-objects", "Toothfish" ] }, { "page": "MOM-class-objects", "title": "MOM class objects", "topics": [ "Albacore_TwoFleet", "MOM-class-objects" ] }, { "page": "AlbacoreExStock", "title": "Albacore Example Stock", "topics": [ "AlbacoreExStock" ] }, { "page": "ApplyAC", "title": "Apply AR(1) autocorrelation to residuals, skipping NAs", "topics": [ "ApplyAC" ] }, { "page": "applyMMP", "title": "Apply multi Management Procedures (class MMP) to a hierarchical list of Data class objects", "topics": [ "applyMMP" ] }, { "page": "applyMP", "title": "Apply Management Procedures to an object of class Data", "topics": [ "applyMP" ] }, { "page": "array_df_conversion", "title": "Convert Between Arrays and Data Frames", "topics": [ "Array2DF", "array_df_conversion", "DF2Array" ] }, { "page": "ArrayOperations", "title": "Perform Operations on Two Arrays", "topics": [ "ArrayDivide", "ArrayExtend", "ArrayFill<-", "ArrayMultiply", "ArrayOperations", "ArraySubtract", "ArraySum" ] }, { "page": "ASAP2OM", "title": "Convert ASAP 3 assessments into an operating model", "topics": [ "ASAP2Data", "ASAP2OM" ] }, { "page": "Assess2MOM", "title": "Reads bootstrap estimates from a stock assessment model into a multi-fleet operating model.", "topics": [ "Assess2MOM" ] }, { "page": "Assess2OM", "title": "Reads bootstrap estimates from a stock assessment model (including VPA) into an operating model. 'Assess2OM' is identical to 'VPA2OM'.", "topics": [ "Assess2OM", "VPA2OM" ] }, { "page": "AsympExFleet", "title": "Asymptotic Selectivity Example Fleet", "topics": [ "AsympExFleet" ] }, { "page": "Data-class-objects", "title": "Data class objects", "topics": [ "Atlantic_mackerel", "China_rockfish", "Cobia", "Data-class-objects", "Example_datafile", "Gulf_blue_tilefish", "ourReefFish", "Red_snapper", "Simulation_1" ] }, { "page": "avail", "title": "What objects of this class are available", "topics": [ "avail" ] }, { "page": "Awatea2OM", "title": "Reads MCMC estimates from Awatea (Paul Starr) processed r file structure into an operating model", "topics": [ "Awatea2OM" ] }, { "page": "BAM2MOM", "title": "Import a multi-stock, multi-fleet OM from a BAM object", "topics": [ "BAM2MOM", "BAM2OM" ] }, { "page": "BAMFleetNames", "title": "Get and Fix BAM Fleet Names", "topics": [ "BAMFleetNames", "FixFleetNames", "GetBAMFleetNames" ] }, { "page": "bio_timeseries", "title": "Extract Biological Time Series", "topics": [ "Biomass", "bio_timeseries", "SBiomass", "SProduction" ] }, { "page": "Bioeconomic", "title": "Bioeconomic", "concept": [ "fleet" ], "topics": [ "Bioeconomic", "Bioeconomic<-", "Cost", "Cost<-", "Depreciation", "Depreciation<-", "Discount", "Discount<-", "Disinvestment", "Disinvestment<-", "Investment", "Investment<-", "Revenue", "Revenue<-" ] }, { "page": "bioeconomic-class", "title": "The 'bioeconomic' S4 Class", "concept": [ "fleet" ], "topics": [ "bioeconomic-class" ] }, { "page": "boxplot.Data", "title": "Boxplot of TAC recommendations", "topics": [ "boxplot.Data" ] }, { "page": "ButterfishExStock", "title": "Butterfish Example Stock", "topics": [ "ButterfishExStock" ] }, { "page": "CalcAgeClasses", "title": "Calculate Age Classes", "topics": [ "CalcAgeClasses" ] }, { "page": "CalcAgeSizeKey", "title": "Calculate an Age-Size Key", "topics": [ "CalcAgeSizeKey" ] }, { "page": "CalcAsymDist", "title": "Calculate the Asymptotic Spatial Distribution of a Movement Matrix", "topics": [ "CalcAsymDist" ] }, { "page": "CalcEquilibrium", "title": "Calculate Absolute Equilibrium Quantities", "topics": [ "CalcEquilibrium" ] }, { "page": "CalcInnovationCov", "title": "Calculate Innovation Covariance Matrix for Multivariate AR(1)", "topics": [ "CalcInnovationCov" ] }, { "page": "CalcMSY", "title": "Calculate MSY Reference Points", "topics": [ "CalcMSY" ] }, { "page": "CalcPerRecruit", "title": "Calculate Per-Recruit Quantities", "topics": [ "CalcPerRecruit" ] }, { "page": "calcRefYield", "title": "Calculate Reference Yield", "topics": [ "calcRefYield" ] }, { "page": "CalcResidualStats", "title": "Calculate residual statistics for log-space index residuals", "topics": [ "CalcResidualStats" ] }, { "page": "CalcSPR0", "title": "Unfished Spawning Production Per Recruit", "topics": [ "CalcSPR0" ] }, { "page": "CalcSurvival", "title": "Calculate Cumulative Survival-at-Age", "topics": [ "CalcSurvival" ] }, { "page": "CalcTSUnits", "title": "Convert Between Season Count and Time Unit Labels", "topics": [ "CalcSeasons", "CalcTSUnits" ] }, { "page": "CalcUnfished_Dynamic", "title": "Calculate Dynamic Unfished Population Dynamics", "topics": [ "CalcUnfished_Dynamic" ] }, { "page": "CalcUnfished_Equilibrium", "title": "Calculate Equilibrium Unfished Population Dynamics", "topics": [ "CalcUnfished_Equilibrium" ] }, { "page": "CalcUnfishedDist", "title": "Calculate the Unfished Spatial Distribution", "topics": [ "CalcUnfishedDist" ] }, { "page": "CalcUnfishedNumber", "title": "Calculate Equilibrium Unfished Number-at-Age", "topics": [ "CalcUnfishedNumber" ] }, { "page": "CalcUnfishedSurvival", "title": "Calculate Unfished Survival", "topics": [ "CalcUnfishedSurvival" ] }, { "page": "CALsimp", "title": "Simplifies the CAL slot of data object", "topics": [ "CALsimp" ] }, { "page": "Can", "title": "Identify management procedures (MPs) based on data availability", "topics": [ "Can", "Cant", "DLMdiag", "Needed" ] }, { "page": "catch_timeseries", "title": "Extract or Assign Catch Time Series", "topics": [ "catch_timeseries", "Discards", "Discards<-", "Interactions", "Landings", "Landings<-", "Removals" ] }, { "page": "Catchability", "title": "Catchability Constructor and Accessors", "concept": [ "fleet" ], "topics": [ "Catchability", "Catchability<-", "Efficiency", "Efficiency<-", "qCV", "qCV<-", "qInc", "qInc<-", "Theta", "Theta<-" ] }, { "page": "catchability-class", "title": "The 'catchability' S4 Class", "concept": [ "fleet" ], "topics": [ "catchability-class" ] }, { "page": "CatchAndSurveyObs", "title": "Catch-and-Survey Observation Model", "concept": [ "obs-examples" ], "topics": [ "CatchAndSurveyObs" ] }, { "page": "catchdata", "title": "CatchData Constructor", "concept": [ "data" ], "topics": [ "CatchData" ] }, { "page": "catchdata-class", "title": "The 'catchdata' S4 Class", "concept": [ "data" ], "topics": [ "catchdata-class" ] }, { "page": "CatchObs", "title": "CatchObs Constructor and Accessors", "concept": [ "obs" ], "topics": [ "CatchObs" ] }, { "page": "catchobs-class", "title": "The 'catchobs' S4 Class", "concept": [ "obs" ], "topics": [ "catchobs-class" ] }, { "page": "CheckCatch", "title": "Check catch data availability and units", "topics": [ "CheckCatch" ] }, { "page": "CheckDuplicate", "title": "Check for duplicated MPs names", "topics": [ "CheckDuplicate" ] }, { "page": "CheckMPs", "title": "Check that specified MPs are valid and will run on MSEtool::SimulatedData", "topics": [ "CheckMPs" ] }, { "page": "checkMSE", "title": "Utility functions for MSE objects", "topics": [ "addMPs", "checkMSE", "joinHist", "joinMSE", "updateMSE" ] }, { "page": "CheckOM", "title": "Check OM object is complete", "topics": [ "CheckOM" ] }, { "page": "CheckPackage", "title": "Check that a required package is installed", "topics": [ "CheckPackage" ] }, { "page": "Choose", "title": "Manually map parameters for the historical period of operating model", "topics": [ "Choose", "ChooseEffort", "ChooseM", "ChooseSelect" ] }, { "page": "CombineFleets", "title": "Combine Multiple Fleets into a Single Fleet", "topics": [ "CombineFleets" ] }, { "page": "CombineMMP", "title": "Create a blank MP recommendations object (class Rec) of the right dimensions", "topics": [ "CombineMMP" ] }, { "page": "CombineOMs", "title": "Combine Multiple Operating Models into One", "topics": [ "CombineOMs" ] }, { "page": "CommercialFleetObs", "title": "Commercial-Fleet Observation Model", "concept": [ "obs-examples" ], "topics": [ "CommercialFleetObs" ] }, { "page": "CompareBAM", "title": "Compare BAM and OM Output", "topics": [ "CompareBAM" ] }, { "page": "CompareSS", "title": "Compare SS3 and OM fishery dynamics", "topics": [ "CompareSS", "CompareSS_Biomass", "CompareSS_Number" ] }, { "page": "compdata", "title": "CompData Constructor", "concept": [ "data" ], "topics": [ "CompData" ] }, { "page": "compdata-class", "title": "The 'compdata' S4 Class", "concept": [ "data" ], "topics": [ "compdata-class" ] }, { "page": "ComplexOM", "title": "Stock Complex Example Operating Model", "concept": [ "om" ], "topics": [ "ComplexOM" ] }, { "page": "CompObs", "title": "CompObs Constructor and Accessors", "concept": [ "obs" ], "topics": [ "CompObs" ] }, { "page": "CompObs-class", "title": "The 'compobs' S4 Class", "concept": [ "obs" ], "topics": [ "CompObs-class", "compobs-class" ] }, { "page": "ControlDefault", "title": "Default OM Control Options", "topics": [ "ControlDefault" ] }, { "page": "Converge", "title": "Check Convergence", "topics": [ "Converge" ] }, { "page": "Convert", "title": "Convert legacy S4 objects to new S4 object classes", "topics": [ "Convert" ] }, { "page": "ConvertData", "title": "Convert a Legacy Data Object to a New data Class", "topics": [ "ConvertData" ] }, { "page": "ConvertFleet", "title": "Convert a Legacy Fleet Object to the Current 'fleet' Class", "topics": [ "ConvertFleet" ] }, { "page": "ConvertImp", "title": "Convert a Legacy Imp Object to a New imp Class", "topics": [ "ConvertImp" ] }, { "page": "ConvertMOM", "title": "Convert Legacy MOM Object to New om Class", "topics": [ "ConvertMOM" ] }, { "page": "ConvertObs", "title": "Convert a Legacy Obs Object to the Current 'obs' Class", "topics": [ "ConvertObs" ] }, { "page": "ConvertOM", "title": "Convert Legacy OM Object to New om Class", "topics": [ "ConvertOM" ] }, { "page": "ConvertStock", "title": "Convert a Legacy Stock Object to the Current 'stock' Class", "topics": [ "ConvertStock" ] }, { "page": "Cos_thresh_tab", "title": "Current default thresholds for COSEWIC satisficing", "topics": [ "Cos_thresh_tab" ] }, { "page": "cparscheck", "title": "Internal function for checking that the 'OM@cpars' is formatted correctly", "topics": [ "cparscheck" ] }, { "page": "Cplot", "title": "Plot the median biomass and yield relative to last historical year", "topics": [ "Cplot" ] }, { "page": "CR2h", "title": "Convert Between Steepness and Compensation Ratio", "topics": [ "CR2h", "h2CR" ] }, { "page": "Data", "title": "Constructor and Accessor for 'Data'", "topics": [ "Data" ] }, { "page": "Data_xl", "title": "Read in Data object from Excel spreadsheet", "topics": [ "Data_xl" ] }, { "page": "Data-class", "title": "The 'data' S4 Class", "topics": [ "data-class" ] }, { "page": "Data-legacy-class", "title": "Class ''Data''", "topics": [ "Data-class", "Data-legacy-class" ] }, { "page": "Data2csv", "title": "Converts a Data object into a .csv data file", "topics": [ "Data2csv" ] }, { "page": "DataDescription", "title": "DataDescription", "topics": [ "DataDescription" ] }, { "page": "DataDir", "title": "Directory of the data in the installed package on your computer", "topics": [ "DataDir" ] }, { "page": "DataHelpers", "title": "Data Helper Functions", "topics": [ "DataHelpers", "LastHistYearInd", "LastTAC", "ProjectionYear" ] }, { "page": "DataInit", "title": "Initialize Data Input Files", "topics": [ "DataInit" ] }, { "page": "DataRichObs", "title": "Data-Rich Observation Model", "concept": [ "obs-examples" ], "topics": [ "DataRichObs" ] }, { "page": "DataSlots", "title": "DataSlots", "topics": [ "DataSlots" ] }, { "page": "DataTrim", "title": "Trim Data Object by Final Year", "topics": [ "DataTrim" ] }, { "page": "Fleet-class-objects", "title": "Fleet class objects", "topics": [ "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" ] }, { "page": "DefaultAges", "title": "Default Ages and Years", "topics": [ "DefaultAges", "DefaultYears" ] }, { "page": "DeleteLogs", "title": "Delete the Log Directory", "topics": [ "DeleteLogs" ] }, { "page": "Depletion", "title": "Depletion Constructor and Accessors", "concept": [ "depletion" ], "topics": [ "Depletion", "Depletion<-", "Final", "Final<-", "Initial", "Initial<-" ] }, { "page": "depletion-class", "title": "The 'depletion' S4 Class", "concept": [ "depletion" ], "topics": [ "depletion-class" ] }, { "page": "DFO_bar", "title": "Department of Fisheries and Oceans stock status bar plot", "topics": [ "DFO_bar" ] }, { "page": "DFO_hist", "title": "Department of Fisheries and Oceans historical plot", "topics": [ "DFO_hist" ] }, { "page": "DFO_plot", "title": "Department of Fisheries and Oceans trade-off plot", "topics": [ "DFO_plot" ] }, { "page": "DFO_plot2", "title": "Department of Fisheries and Oceans default plot 2", "topics": [ "DFO_plot2" ] }, { "page": "DFO_proj", "title": "Department of Fisheries and Oceans projection plot", "topics": [ "DFO_proj" ] }, { "page": "DFO_quant", "title": "Department of Fisheries and Oceans biomass quantile plot", "topics": [ "DFO_quant" ] }, { "page": "DFO_report", "title": "Create a standard DFO MSE report", "topics": [ "DFO_report" ] }, { "page": "DFO_spider", "title": "DFO performance spider plot (top three MPs)", "topics": [ "DFO_spider" ] }, { "page": "DFO_tab", "title": "Create a standard DFO performance table", "topics": [ "DFO_tab" ] }, { "page": "DFO_tab_formatted", "title": "A formatted version of the standard DFO performance plot, color coded by thresholds", "topics": [ "DFO_tab_formatted" ] }, { "page": "dim", "title": "Dimensions of an Object", "topics": [ "dim" ] }, { "page": "dimension-utils", "title": "Add or Drop Named Dimensions of an Array", "topics": [ "AddDimension", "dimension-utils", "DropDimension" ] }, { "page": "DiscardMortality", "title": "Discard Mortality", "concept": [ "fleet" ], "topics": [ "DiscardMortality", "DiscardMortality<-" ] }, { "page": "discardmortality-class", "title": "The 'discardmortality' S4 Class", "concept": [ "fleet" ], "topics": [ "discardmortality-class" ] }, { "page": "DLMDataDir", "title": "Directory of the installed package on your computer", "topics": [ "DLMDataDir" ] }, { "page": "doHCR", "title": "Hockey Stick Harvest control rule that modifies TAC.", "topics": [ "doHCR" ] }, { "page": "doIfreq", "title": "Create indices that are sampled at various frequencies", "topics": [ "doIfreq" ] }, { "page": "Dom", "title": "Determine dominate MPs", "topics": [ "Dom" ] }, { "page": "DomeExFleet", "title": "Dome-Shaped Selectivity Example Fleet", "topics": [ "DomeExFleet" ] }, { "page": "doRec", "title": "Calculate a management recommendation given constraints", "topics": [ "doRec" ] }, { "page": "Effort", "title": "Effort Constructor and Accessors", "concept": [ "fleet" ], "topics": [ "AnglerPerTrip", "AnglerPerTrip<-", "Distribution", "Distribution<-", "Effort", "Effort<-", "Maximum", "Maximum<-", "Mode", "Mode<-", "Targeting", "Targeting<-", "TripsScalar", "TripsScalar<-" ] }, { "page": "effort-class", "title": "The 'effort' S4 Class", "concept": [ "fleet" ], "topics": [ "effort-class" ] }, { "page": "effortdata", "title": "EffortData Constructor and Accessors", "concept": [ "data" ], "topics": [ "EffortData" ] }, { "page": "effortdata-class", "title": "The 'effortdata' S4 Class", "concept": [ "data" ], "topics": [ "effortdata-class" ] }, { "page": "EffortObs", "title": "EffortObs Constructor and Accessors", "concept": [ "obs" ], "topics": [ "EffortObs" ] }, { "page": "effortobs-class", "title": "The 'effortobs' S4 Class", "concept": [ "obs" ], "topics": [ "effortobs-class" ] }, { "page": "Emp", "title": "A flexible empirical management procedure.", "topics": [ "Emp" ] }, { "page": "EmptyObject", "title": "Test Whether an Object is Empty", "topics": [ "EmptyObject" ] }, { "page": "equilibrium-class", "title": "The 'equilibrium' S4 Class", "topics": [ "equilibrium-class" ] }, { "page": "ExampleMPs", "title": "Example Management Procedures", "topics": [ "AverageCatch", "CurrentCatch", "CurrentEffort", "CurrentLandings", "ExampleMPs" ] }, { "page": "exploitationdata-class", "title": "'exploitationdata' Class", "topics": [ "ExploitationData", "exploitationdata-class" ] }, { "page": "ExploitationObs", "title": "ExploitationObs Constructor", "concept": [ "obs" ], "topics": [ "ExploitationObs" ] }, { "page": "exploitationobs-class", "title": "The 'exploitationobs' S4 Class", "concept": [ "obs" ], "topics": [ "exploitationobs-class" ] }, { "page": "Extend", "title": "Extend an Array Along Named Dimensions", "topics": [ "Extend", "ExtendAges", "ExtendAreas", "ExtendClasses", "ExtendSims", "ExtendYears" ] }, { "page": "extract-unfished", "title": "Unfished Reference Point Quantities", "topics": [ "B0", "extract-unfished", "N0", "SB0", "SP0" ] }, { "page": "Fease", "title": "MP feasibility diagnostic", "topics": [ "Fease" ] }, { "page": "Fecundity", "title": "Fecundity Constructor and Accessors", "concept": [ "fecundity" ], "topics": [ "Fecundity", "Fecundity<-" ] }, { "page": "fecundity-class", "title": "The 'fecundity' S4 Class", "concept": [ "fecundity" ], "topics": [ "fecundity-class" ] }, { "page": "Fecundity-Models", "title": "Fecundity Models", "topics": [ "Fecundity-Models", "FecundityAtAge", "FecundityAtLength", "FecundityAtWeight", "FecundityModels", "FecundityModelsAge", "FecundityModelsLength", "FecundityModelsWeight" ] }, { "page": "F_timeseries", "title": "Extract Fishing Mortality Time Series", "topics": [ "FDead", "FInteract", "FRetain", "F_timeseries" ] }, { "page": "FitMovement", "title": "Fit a Movement Matrix to Target Spatial Parameters", "topics": [ "FitMovement" ] }, { "page": "FitStockTargeting", "title": "Fit statistical properties of historical stock targeting", "topics": [ "FitStockTargeting" ] }, { "page": "Fleet", "title": "Fleet", "concept": [ "fleet" ], "topics": [ "Closure", "Closure<-", "Fleet", "Fleet<-", "WeightFleet", "WeightFleet<-" ] }, { "page": "Fleet-class", "title": "The 'fleet' S4 Class", "concept": [ "fleet" ], "topics": [ "fleet-class" ] }, { "page": "Fleet-legacy-class", "title": "Class ''Fleet''", "topics": [ "Fleet-class", "Fleet-legacy-class" ] }, { "page": "FleetDescription", "title": "FleetDescription", "topics": [ "FleetDescription" ] }, { "page": "FMSYref", "title": "Reference management procedures", "topics": [ "curEref", "FMSYref", "FMSYref50", "FMSYref75", "NFref" ] }, { "page": "GenerateStockTargeting", "title": "Generate Stochastic Stock Targeting Trajectories", "topics": [ "GenerateStockTargeting" ] }, { "page": "Obs-class-objects", "title": "Obs class objects", "topics": [ "Generic_Obs", "Imprecise_Biased", "Imprecise_Unbiased", "Obs-class-objects", "Perfect_Info", "Precise_Biased", "Precise_Unbiased" ] }, { "page": "GenHistEffort", "title": "Generate Stochastic Historical Effort Time Series", "topics": [ "GenHistEffort" ] }, { "page": "GenMeanAtLength", "title": "Generate Mean-at-Age, Length, or Weight Arrays", "topics": [ "GenMeanAtAge", "GenMeanAtLength", "GenMeanAtWeight" ] }, { "page": "GenMultiStockRecDevs", "title": "Generate Correlated Multi-Stock Recruitment Deviations", "topics": [ "GenMultiStockRecDevs" ] }, { "page": "GenRecDevs", "title": "Generate Stock-Recruitment Deviations", "topics": [ "GenRecDevs" ] }, { "page": "GenResiduals", "title": "Generate (log-space) residuals with truncated log-normal distribution", "topics": [ "GenResiduals" ] }, { "page": "getclass", "title": "get object class", "topics": [ "getclass" ] }, { "page": "getDataList", "title": "Get part of an MP specific data-list", "topics": [ "getDataList" ] }, { "page": "getfirstlev", "title": "Extract the first dimension of a hierarchical list of recommendation objects", "topics": [ "getfirstlev" ] }, { "page": "GetMetaData", "title": "Retrieve Operating Model Metadata", "topics": [ "GetMetaData" ] }, { "page": "getmov2", "title": "Optimization function to find a movement model that matches user specified movement characteristics modified for Rcpp.", "topics": [ "getmov2" ] }, { "page": "getMP", "title": "Search R session for MP", "topics": [ "getMP" ] }, { "page": "getnIVs", "title": "Count independent variables for a MICE relationship at position x in a Rel list", "topics": [ "getnIVs" ] }, { "page": "getsel", "title": "Calculate selectivity curve", "topics": [ "getsel" ] }, { "page": "GetSSRefPoints", "title": "Get Reference Points from Stock Synthesis Output", "topics": [ "GetSSRefPoints" ] }, { "page": "hconv", "title": "Stock recruit parameterization", "topics": [ "hconv", "R0conv", "SRalphaconv", "SRbetaconv" ] }, { "page": "Herm-int", "title": "Internal Herm functions", "topics": [ "checkHerm", "expandHerm", "Herm-int", "subsetHerm" ] }, { "page": "Hist", "title": "'hist' Class and Accessor", "topics": [ "Hist" ] }, { "page": "Hist-class", "title": "'hist' Class", "topics": [ "hist-class" ] }, { "page": "Hist-legacy-class", "title": "Class ''Hist''", "topics": [ "Hist-class", "Hist-legacy-class" ] }, { "page": "hist2", "title": "Wrapper for histogram function", "topics": [ "hist2" ] }, { "page": "HistDescription", "title": "HistDescription", "topics": [ "HistDescription" ] }, { "page": "Imp", "title": "Imp Constructor and Accessor", "concept": [ "imp" ], "topics": [ "Imp" ] }, { "page": "Imp-class", "title": "Implementation Error", "concept": [ "imp" ], "topics": [ "imp-class" ] }, { "page": "Imp-legacy-class", "title": "Class ''Imp''", "topics": [ "Imp-class", "Imp-legacy-class" ] }, { "page": "ImpDescription", "title": "ImpDescription", "topics": [ "ImpDescription" ] }, { "page": "ImportBAM", "title": "Import BAM Output into an Operating Model", "topics": [ "GetBAMOutput", "ImportBAM", "ListBAMStocks" ] }, { "page": "ImportBAMData", "title": "Import BAM Assessment Data into an Operating Model", "topics": [ "ImportBAMData" ] }, { "page": "ImportSS", "title": "Import a Stock Synthesis Model into an Operating Model", "topics": [ "ImportSS" ] }, { "page": "ImportSSData", "title": "Import SS3 data into a Data object", "topics": [ "ImportSSData" ] }, { "page": "ImportSSReport", "title": "Import SS3 Report directories with optional parallel processing", "topics": [ "ImportSSReport" ] }, { "page": "ImpSlot", "title": "ImpSlot Constructor and Accessors", "concept": [ "imp" ], "topics": [ "ImpSlot" ] }, { "page": "indicesdata-class", "title": "The 'indicesdata' S4 Class", "topics": [ "indicesdata-class" ] }, { "page": "IndicesObs", "title": "IndicesObs Constructor and Accessors", "concept": [ "obs" ], "topics": [ "IndicesObs" ] }, { "page": "indicesobs-class", "title": "The 'indicesobs' S4 Class", "concept": [ "obs" ], "topics": [ "indicesobs-class" ] }, { "page": "initialize-methods", "title": "~~ Methods for Function 'initialize' ~~", "topics": [ "initialize-methods" ] }, { "page": "Input", "title": "Function to run a set of input control methods", "topics": [ "Input" ] }, { "page": "iSCAM", "title": "Reads iSCAM files into a hierarchical R list object", "topics": [ "fetch.file.names", "iSCAM", "load.iscam.files", "read.control.file", "read.data.file", "read.mcmc", "read.par.file", "read.projection.file", "read.report.file" ] }, { "page": "iSCAM2OM", "title": "Reads MPD or MCMC estimates and data from iSCAM file structure into an operating model", "topics": [ "iSCAM2Data", "iSCAM2OM" ] }, { "page": "iSCAMcomps", "title": "Combines all iSCAM age composition data across fleets", "topics": [ "iSCAMcomps" ] }, { "page": "iSCAMinds", "title": "Combines indices into a single index using linear modelling (** Deprecated **)", "topics": [ "iSCAMinds" ] }, { "page": "isNewObject", "title": "Test Whether an Object is a Default-Constructed Instance", "topics": [ "isNewObject" ] }, { "page": "join_plots", "title": "Plot several plots with a shared legend", "topics": [ "join_plots" ] }, { "page": "joinData", "title": "Join Data objects present in a list", "topics": [ "joinData" ] }, { "page": "JoinYear", "title": "Join Two Objects Along the Year Dimension", "topics": [ "JoinYear" ] }, { "page": "Kplot", "title": "KOBE plot: a projection by projection plot of F/FMSY and B/BMSY", "topics": [ "Kplot" ] }, { "page": "Lag_Data", "title": "Lag the time-series slots in a 'Data' object by a specified number of time-steps", "topics": [ "Lag_Data" ] }, { "page": "ldim", "title": "Dimensions of a hierarchical list object", "topics": [ "ldim" ] }, { "page": "Length", "title": "Length Constructor and Accessors", "concept": [ "length" ], "topics": [ "ALK", "ALK<-", "Length", "Length<-" ] }, { "page": "Length-at-Age-Models", "title": "Length-at-Age Growth Models", "topics": [ "Brody", "Gompertz", "Length-at-Age-Models", "LengthModels", "Schnute", "vonBert" ] }, { "page": "length-class", "title": "The 'length' S4 Class", "concept": [ "length" ], "topics": [ "length-class" ] }, { "page": "LengthStructuredObs", "title": "Length-Structured Observation Model", "concept": [ "obs-examples" ], "topics": [ "LengthStructuredObs" ] }, { "page": "LH2OM", "title": "Predict missing life-history parameters", "topics": [ "LH2OM", "predictLH" ] }, { "page": "LHdatabase", "title": "LHdatabase", "topics": [ "LHdatabase" ] }, { "page": "lifehistorydata-class", "title": "'lifehistorydata' Class", "topics": [ "LifeHistoryData", "lifehistorydata-class" ] }, { "page": "LifeHistoryObs", "title": "LifeHistoryObs Constructor", "concept": [ "obs" ], "topics": [ "LifeHistoryObs" ] }, { "page": "lifehistoryobs-class", "title": "The 'lifehistoryobs' S4 Class", "concept": [ "obs" ], "topics": [ "lifehistoryobs-class" ] }, { "page": "list-array-conversion", "title": "Convert Between Lists and Arrays", "topics": [ "Array2List", "list-array-conversion", "List2Array" ] }, { "page": "LoadArgs", "title": "Load Function Arguments into an Environment", "topics": [ "LoadArgs" ] }, { "page": "Log", "title": "Display Log Warnings", "topics": [ "Log" ] }, { "page": "logit", "title": "Logit and Inverse Logit (Sigmoid) Functions", "topics": [ "ilogit", "logit" ] }, { "page": "makeMOM", "title": "Utility for making multi-OMs", "topics": [ "makeMOM" ] }, { "page": "makemov", "title": "Calculates movement matrices from user inputs for fraction in each area (fracs) and probability of staying in areas (prob)", "topics": [ "makemov" ] }, { "page": "makemov2", "title": "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.", "topics": [ "makemov2" ] }, { "page": "makeRel", "title": "MICE relationships for multi-OM", "topics": [ "makeRel", "predict.Rel", "print.Rel", "simulate.Rel" ] }, { "page": "makeTransparent", "title": "Make colors transparent", "topics": [ "makeTransparent" ] }, { "page": "Maturity", "title": "Maturity Constructor and Accessors", "concept": [ "maturity" ], "topics": [ "Maturity", "Maturity<-", "Semelparous", "Semelparous<-" ] }, { "page": "maturity-class", "title": "The 'maturity' S4 Class", "concept": [ "maturity" ], "topics": [ "maturity-class" ] }, { "page": "Maturity-Models", "title": "Maturity Models: Age, Length, and Weight", "topics": [ "Maturity-Models", "MaturityAtAge", "MaturityAtLength", "MaturityAtWeight", "MaturityModels", "MaturityModelsAge", "MaturityModelsLength", "MaturityModelsWeight" ] }, { "page": "ML2D", "title": "Depletion and F estimation from mean length of catches", "topics": [ "ML2D" ] }, { "page": "MMSE-legacy-class", "title": "Class ''MMSE''", "topics": [ "MMSE-class", "MMSE-legacy-class" ] }, { "page": "model-helpers", "title": "Selectivity, Retention, Weight, Fecundity, and Maturity Model Helpers", "topics": [ "allometric", "dnormal", "double_normal", "logistic_50_95", "model-helpers" ] }, { "page": "MOM-legacy-class", "title": "Class ''MOM''", "topics": [ "MOM-class", "MOM-legacy-class" ] }, { "page": "movestockCPP", "title": "Apply the movement model to the stock for one time-step", "topics": [ "movestockCPP" ] }, { "page": "movfit_Rcpp", "title": "Rcpp version of the Optimization function that returns the squared difference between user specified and calculated movement parameters.", "topics": [ "movfit_Rcpp" ] }, { "page": "MPCalcsNAs", "title": "Fill any NAs arising from MPCalcs (hermaphroditism mode)", "topics": [ "MPCalcsNAs" ] }, { "page": "MPtype", "title": "Management Procedure Type", "topics": [ "MPtype" ] }, { "page": "MSE-class", "title": "'mse' Class", "topics": [ "mse-class" ] }, { "page": "MSE-legacy-class", "title": "Class ''MSE''", "topics": [ "MSE-class", "MSE-legacy-class" ] }, { "page": "MSE2Slick", "title": "Convert an 'mse' Object to a Slick Object", "topics": [ "MSE2Slick" ] }, { "page": "MSEDescription", "title": "MSEDescription", "topics": [ "MSEDescription" ] }, { "page": "MSEextra", "title": "Load more data from MSEextra package", "topics": [ "MSEextra" ] }, { "page": "MSY-accessors", "title": "Access MSY Reference Point Slots", "topics": [ "BMSY", "FMSY", "MSY-accessors", "MSYDiscards", "MSYLandings", "MSYRefs", "SBMSY", "SPMSY", "SPRMSY" ] }, { "page": "MSYCalcs", "title": "Internal function to calculate MSY Reference Points", "topics": [ "MSYCalcs" ] }, { "page": "multiData", "title": "Combine data among fleets", "topics": [ "multiData" ] }, { "page": "multiDataS", "title": "Combine data among stocks", "topics": [ "multiDataS" ] }, { "page": "multidebug", "title": "A basic comparison of runMSE output (MSE) and multiMSE (MMSE)", "topics": [ "multidebug" ] }, { "page": "MultiStockOM", "title": "Multi-Stock Multi-Fleet Example Operating Model", "concept": [ "om" ], "topics": [ "MultiStockOM" ] }, { "page": "name-accessors", "title": "Access Stock or Fleet Names", "topics": [ "FleetNames", "name-accessors", "StockNames" ] }, { "page": "NaturalMortality", "title": "NaturalMortality Constructor and Accessors", "concept": [ "naturalmortality" ], "topics": [ "NaturalMortality", "NaturalMortality<-" ] }, { "page": "naturalmortality-class", "title": "The 'naturalmortality' S4 Class", "concept": [ "naturalmortality" ], "topics": [ "naturalmortality-class" ] }, { "page": "NaturalMortality-Models", "title": "Natural Mortality Models", "topics": [ "LorenzenMortalityLength", "LorenzenMortalityWeight", "MortalityAtAge", "NaturalMortality-Models", "NaturalMortalityModels" ] }, { "page": "NIL", "title": "Item in list: get the list values from a list of lists", "topics": [ "NIL" ] }, { "page": "NOAA_plot", "title": "National Oceanographic and Atmospheric Administration default plot 1", "topics": [ "NOAA_plot" ] }, { "page": "Number", "title": "Extract Number-at-Age time series", "topics": [ "Number" ] }, { "page": "Obs", "title": "Obs Constructor and Accessor", "concept": [ "obs" ], "topics": [ "Obs", "Obs<-" ] }, { "page": "Obs-class", "title": "The 'obs' S4 Class", "concept": [ "obs" ], "topics": [ "obs-class" ] }, { "page": "Obs-legacy-class", "title": "Class ''Obs''", "topics": [ "Obs-class", "Obs-legacy-class" ] }, { "page": "ObsDescription", "title": "ObsDescription", "topics": [ "ObsDescription" ] }, { "page": "OM", "title": "OM Constructor and Accessor", "concept": [ "om" ], "topics": [ "OM" ] }, { "page": "OM-accessors", "title": "Access and Modify OM Slots", "concept": [ "om" ], "topics": [ "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<-" ] }, { "page": "om-class", "title": "The 'om' S4 Class", "concept": [ "om" ], "topics": [ "om-class" ] }, { "page": "OM-legacy-class", "title": "Class ''OM''", "topics": [ "OM-class", "OM-legacy-class" ] }, { "page": "OMDescription", "title": "OMDescription", "topics": [ "OMDescription" ] }, { "page": "OMdoc", "title": "Generate OM Documentation Report", "topics": [ "OMdoc" ] }, { "page": "OMexample", "title": "Copy example OM XL and OM Documentation", "topics": [ "OMexample" ] }, { "page": "OMinit", "title": "Initialize Operating Model", "topics": [ "OMinit" ] }, { "page": "optCPU", "title": "Determine optimal number of cpus", "topics": [ "optCPU" ] }, { "page": "Imp-class-objects", "title": "Imp class objects", "topics": [ "Imp-class-objects", "Overages", "Perfect_Imp" ] }, { "page": "PerformanceMetric", "title": "Performance Metrics Methods", "topics": [ "AAVE", "AAVY", "LTY", "P10", "P100", "P50", "PerformanceMetric", "PGK", "PNOF", "STY", "Yield" ] }, { "page": "perrecruit-class", "title": "The 'perrecruit' S4 Class", "topics": [ "perrecruit-class" ] }, { "page": "plot.Data", "title": "Plot Data object", "topics": [ "plot.Data" ] }, { "page": "plot.MMSE", "title": "Standard plot for an object of class MMSE (multi MSE)", "topics": [ "plot.MMSE" ] }, { "page": "plot.MOM", "title": "Standard plot for an object of class MOM", "topics": [ "plot,MOM,missing-method", "plot.MOM" ] }, { "page": "plot.MSE", "title": "Plot MSE object", "topics": [ "plot.MSE" ] }, { "page": "plot.Stock", "title": "Plot Operating Model Object", "topics": [ "plot.Fleet", "plot.Hist", "plot.Imp", "plot.Obs", "plot.OM", "plot.pars", "plot.Stock" ] }, { "page": "plotFun", "title": "Print out plotting functions", "topics": [ "plotFun" ] }, { "page": "plotmulti", "title": "A basic SSB plot for debugging runMSE output", "topics": [ "plotmulti" ] }, { "page": "plotOFL", "title": "A generic OFL plot for NOAA use", "topics": [ "plotOFL" ] }, { "page": "plotquant", "title": "A fairly tidy time-series quantile plot", "topics": [ "plotquant" ] }, { "page": "plotRel", "title": "Plot a relationship between stocks", "topics": [ "plotRel" ] }, { "page": "PMLimit", "title": "Create a table of Performance Limits and Performance Objectives", "topics": [ "PMLimit", "PMObj" ] }, { "page": "PMobj-class", "title": "An object for storing data for analysis using data-limited methods", "topics": [ "PMobj-class" ] }, { "page": "popdynamics-class", "title": "'popdynamics' Class", "topics": [ "popdynamics", "popdynamics-class" ] }, { "page": "Populate", "title": "Populate Operating Model Components", "topics": [ "Populate" ] }, { "page": "PopulateCatchability", "title": "Populate a Catchability Object", "topics": [ "PopulateCatchability" ] }, { "page": "PopulateCatchObs", "title": "Populate Catch Observation Error", "topics": [ "PopulateCatchObs" ] }, { "page": "PopulateClosure", "title": "Populate a Closure Object", "topics": [ "PopulateClosure" ] }, { "page": "PopulateCompObs", "title": "Populate Composition Observation Error", "topics": [ "PopulateCompObs" ] }, { "page": "PopulateDepletion", "title": "Populate a Depletion Object", "topics": [ "PopulateDepletion" ] }, { "page": "PopulateDiscardMortality", "title": "Populate a DiscardMortality Object", "topics": [ "PopulateDiscardMortality" ] }, { "page": "PopulateEffort", "title": "Populate an Effort Object", "topics": [ "PopulateEffort" ] }, { "page": "PopulateEffortObs", "title": "Populate Effort Observation Error", "topics": [ "PopulateEffortObs" ] }, { "page": "PopulateFecundity", "title": "Populate a Fecundity Object", "topics": [ "PopulateFecundity" ] }, { "page": "PopulateFleet", "title": "Populate a Fleet Object", "topics": [ "PopulateFleet" ] }, { "page": "PopulateIndexObs", "title": "Populate Index Observation Error", "topics": [ "PopulateIndexObs" ] }, { "page": "PopulateLength", "title": "Populate a Length Object", "topics": [ "PopulateLength" ] }, { "page": "PopulateMaturity", "title": "Populate a Maturity Object", "topics": [ "PopulateMaturity" ] }, { "page": "PopulateNaturalMortality", "title": "Populate a Natural Mortality Object", "topics": [ "PopulateNaturalMortality" ] }, { "page": "PopulateObs", "title": "Populate an Obs Object", "topics": [ "PopulateObs" ] }, { "page": "PopulateOM", "title": "Populate an Operating Model", "topics": [ "PopulateOM" ] }, { "page": "PopulateRetention", "title": "Populate a Retention Object", "topics": [ "PopulateRetention" ] }, { "page": "PopulateSelectivity", "title": "Populate a Selectivity Object", "topics": [ "PopulateSelectivity" ] }, { "page": "PopulateSpatial", "title": "Populate a Spatial Object", "topics": [ "PopulateSpatial" ] }, { "page": "PopulateSRR", "title": "Populate an SRR Object", "topics": [ "PopulateSRR" ] }, { "page": "PopulateStock", "title": "Populate a Stock Object", "topics": [ "PopulateStock" ] }, { "page": "PopulateWeight", "title": "Populate a Weight-at-Age Object", "topics": [ "PopulateWeight" ] }, { "page": "populating-schedules", "title": "Specifying Biological and Fleet Schedules", "topics": [ "pars-model-meanatage", "populating-schedules", "schedule-population" ] }, { "page": "PPD", "title": "Extract and Reconstruct Posterior Predicted Data (PPD)", "topics": [ "PPD" ] }, { "page": "Pplot", "title": "A projection by projection plot of F/FMSY and B/BMSY", "topics": [ "Pplot" ] }, { "page": "Pplot2", "title": "A projection by projection plot of F/FMSY, B/BMSY, B/B0, and yield", "topics": [ "Pplot2" ] }, { "page": "print.multiHist", "title": "Print method for 'multiHist' objects", "topics": [ "print.multiHist" ] }, { "page": "print.RepList", "title": "Print a 'RepList' object", "topics": [ "print.RepList" ] }, { "page": "Project", "title": "Project an Operating Model Over the Projection Period", "topics": [ "Project" ] }, { "page": "PWhisker", "title": "Performance Whisker Plot", "topics": [ "PWhisker" ] }, { "page": "quantile_plot", "title": "A quantile plot", "topics": [ "quantile_plot" ] }, { "page": "rDirichletMultinomial", "title": "Dirichlet-Multinomial Sampler", "topics": [ "rDirichletMultinomial" ] }, { "page": "RealFease", "title": "MP feasibility diagnostic using real data", "topics": [ "RealFease" ] }, { "page": "Rec-class", "title": "Class ''Rec''", "topics": [ "Rec-class" ] }, { "page": "ReduceDims", "title": "Reduce redundant Sim, Year, and Age dimensions in arrays", "topics": [ "ReduceDims" ] }, { "page": "ReduceNSim", "title": "Reduce the number of simulations", "topics": [ "ReduceNSim" ] }, { "page": "reference-class", "title": "Reference Points Object", "topics": [ "reference-class" ] }, { "page": "referencedata-class", "title": "'referencedata' Class", "topics": [ "ReferenceData", "referencedata-class" ] }, { "page": "refpointsMSY-class", "title": "The 'refpointsMSY' S4 Class", "topics": [ "refpointsMSY-class" ] }, { "page": "Rename", "title": "Rename Stocks and Fleets in an OM", "topics": [ "Rename" ] }, { "page": "Reorder", "title": "Reorder Stocks and Fleets in an OM", "topics": [ "Reorder" ] }, { "page": "Replace", "title": "Replace an existing Stock, Fleet, Obs, or Imp object", "topics": [ "Replace" ] }, { "page": "replic8", "title": "Enlarge (replicate) a DLM data object to create an additional dimension for simulation / sensitivity testing", "topics": [ "replic8" ] }, { "page": "Report", "title": "Generate a Data Report", "topics": [ "Report" ] }, { "page": "ReqData", "title": "ReqData", "topics": [ "ReqData" ] }, { "page": "Required", "title": "What management procedures need what data", "topics": [ "Required" ] }, { "page": "Retention", "title": "Retention", "concept": [ "fleet" ], "topics": [ "Retention", "Retention<-" ] }, { "page": "retention-class", "title": "The 'retention' S4 Class", "concept": [ "fleet" ], "topics": [ "retention-class" ] }, { "page": "Retention-Models", "title": "Retention Models", "topics": [ "DoubleNormalRetention", "DoubleNormalRetentionWeight", "Retention-Models", "RetentionAtAge", "RetentionAtLength", "RetentionAtWeight", "RetentionKnifeEdgeAge", "RetentionKnifeEdgeLength", "RetentionModels", "RetentionModelsAge", "RetentionModelsLength", "RetentionModelsWeight" ] }, { "page": "runCOSEWIC", "title": "COSEWIC MSE run using the correct MPs and projected time horizon", "topics": [ "COSEWIC_Blow", "COSEWIC_Dplot", "COSEWIC_Hplot", "COSEWIC_Pplot", "COSEWIC_report", "COSEWIC_tab", "COSEWIC_tab_formatted", "runCOSEWIC" ] }, { "page": "runInMP", "title": "Runs input control MPs on a Data object.", "topics": [ "runInMP" ] }, { "page": "runMP", "title": "Run a Management Procedure", "topics": [ "runMP" ] }, { "page": "runMSE", "title": "Run a Management Strategy Evaluation", "topics": [ "runMSE" ] }, { "page": "S4SlotSizes", "title": "Summarise S4 Object Memory Usage by Slot", "topics": [ "S4SlotSizes" ] }, { "page": "Save", "title": "Save an Object to Disk", "topics": [ "Save" ] }, { "page": "select_MP", "title": "Select DataList for an MP from 'MMSE@PPD'", "topics": [ "select_MP" ] }, { "page": "Selectivity", "title": "Selectivity", "concept": [ "fleet" ], "topics": [ "isRel", "isRel<-", "Selectivity", "Selectivity<-" ] }, { "page": "selectivity-class", "title": "The 'selectivity' S4 Class", "concept": [ "fleet" ], "topics": [ "selectivity-class" ] }, { "page": "Selectivity-Models", "title": "Selectivity Models", "topics": [ "DoubleNormal", "DoubleNormalWeight", "Selectivity-Models", "SelectivityAtAge", "SelectivityAtLength", "SelectivityAtWeight", "SelectivityKnifeEdgeAge", "SelectivityKnifeEdgeLength", "SelectivityModels", "SelectivityModelsAge", "SelectivityModelsLength", "SelectivityModelsWeight" ] }, { "page": "Sense", "title": "Sensitivity analysis", "topics": [ "Sense" ] }, { "page": "setup", "title": "Setup parallel processing", "topics": [ "setup" ] }, { "page": "SetupParallel", "title": "Set Up Parallel Processing for openMSE Workflows", "topics": [ "CheckParallel", "DisableParallel", "SetupParallel" ] }, { "page": "show-methods", "title": "Show Methods", "topics": [ "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" ] }, { "page": "show-MSEtool", "title": "Show MSEtool S4 objects", "topics": [ "show", "show,Data-method", "show,Hist-method", "show,MMSE-method", "show,MOM-method", "show,MSE-method", "show,OM-method", "show-MSEtool" ] }, { "page": "show-MSE", "title": "Show the output of a PM", "topics": [ "show,PMobj-method" ] }, { "page": "show-Rec", "title": "Show the output of a single MP recommendation", "topics": [ "show,Rec-method" ] }, { "page": "SIL", "title": "Slot in list: get the slot values from a list of objects", "topics": [ "SIL" ] }, { "page": "simCAA", "title": "Simulate Catch-at-Age Data", "topics": [ "simCAA" ] }, { "page": "simCAL", "title": "Simulate Catch-at-Length Data", "topics": [ "simCAL" ] }, { "page": "simmov", "title": "Calculates movement matrices from user inputs", "topics": [ "plot_mov", "simmov" ] }, { "page": "simmov2", "title": "Calculates movement matrices from user specified distribution among other areas", "topics": [ "simmov2" ] }, { "page": "Simulate", "title": "Simulate Operating Model Dynamics", "topics": [ "Simulate" ] }, { "page": "SimulatedData", "title": "SimulatedData Data", "topics": [ "SimulatedData" ] }, { "page": "multiMSE", "title": "Run a multi-fleet multi-stock Management Strategy Evaluation", "topics": [ "multiMSE", "ProjectMOM", "SimulateMOM" ] }, { "page": "SingleStockOM", "title": "Single Stock Example Operating Model", "concept": [ "om" ], "topics": [ "SingleStockOM" ] }, { "page": "SketchFun", "title": "Manually map the historical relative fishing effort trajectory.", "topics": [ "SketchFun" ] }, { "page": "smoothy", "title": "General purpose polynomial smoother", "topics": [ "smoothy" ] }, { "page": "Spatial", "title": "Spatial Constructor and Accessors", "concept": [ "spatial" ], "topics": [ "Arrangement", "Arrangement<-", "CVDist", "CVDist<-", "CVStay", "CVStay<-", "FracOther", "FracOther<-", "Movement", "Movement<-", "ProbStaying", "ProbStaying<-", "RelativeSize", "RelativeSize<-", "Spatial", "Spatial<-", "UnfishedDist", "UnfishedDist<-" ] }, { "page": "spatial-class", "title": "The 'spatial' S4 Class", "concept": [ "spatial" ], "topics": [ "spatial-class" ] }, { "page": "Splot", "title": "Standard MSE projection plot", "topics": [ "Splot" ] }, { "page": "SRR", "title": "SRR Constructor and Accessors", "concept": [ "srr" ], "topics": [ "R0", "R0<-", "RecDevHist", "RecDevHist<-", "RecDevInit", "RecDevInit<-", "RecDevProj", "RecDevProj<-", "RelRecFun", "RelRecFun<-", "SpawnTimeFrac", "SpawnTimeFrac<-", "SPFrom", "SPFrom<-", "SRR", "SRR<-" ] }, { "page": "srr-class", "title": "The 'srr' S4 Class", "concept": [ "srr" ], "topics": [ "srr-class" ] }, { "page": "SRRModels", "title": "Stock–Recruitment Relationships (SRR)", "topics": [ "BevertonHolt", "BevertonHolt_RelRec", "HockeyStick", "HockeyStick_RelRec", "Ricker", "Ricker_RelRec", "SRRModels" ] }, { "page": "SS2Data", "title": "Reads data Stock Synthesis file structure into a Data object using package r4ss", "topics": [ "SS2Data" ] }, { "page": "SS2DataMOM", "title": "Reads data Stock Synthesis file structure into a nested Data object analogous with multiMSE", "topics": [ "SS2DataMOM" ] }, { "page": "SS2MOM", "title": "Import Stock Synthesis to MOM (2-sex multi-fleet) or OM (single-sex, single-fleet)", "topics": [ "MOM_agg_fleets", "plot_SS2MOM", "plot_SS2OM", "SS2MOM", "SS2OM", "SSMOM2OM" ] }, { "page": "SSBrefplot", "title": "Plot Spawning stock biomass and reference points for both historical and projected period", "topics": [ "SSBrefplot" ] }, { "page": "StandardizeEffort", "title": "Standardize fishing effort across stocks for each fleet", "topics": [ "StandardizeEffort" ] }, { "page": "Stock", "title": "Stock Constructor and Accessors", "concept": [ "stock" ], "topics": [ "CommonName", "CommonName<-", "Species", "Species<-", "Stock", "Stock<-" ] }, { "page": "Stock-class", "title": "The 'stock' S4 Class", "concept": [ "stock" ], "topics": [ "stock-class" ] }, { "page": "Stock-legacy-class", "title": "Class ''Stock''", "topics": [ "Stock-class", "Stock-legacy-class" ] }, { "page": "StockDescription", "title": "StockDescription", "topics": [ "StockDescription" ] }, { "page": "StockTargeting", "title": "Stock Targeting Constructor", "topics": [ "StockTargeting" ] }, { "page": "stocktargeting-class", "title": "The 'stocktargeting' S4 Class", "topics": [ "stocktargeting-class" ] }, { "page": "Sub", "title": "Subset MSE object by management procedure (MP) or simulation.", "topics": [ "Sub" ] }, { "page": "SubCpars", "title": "Subset the cpars slot in an operating model", "topics": [ "SubCpars", "SubCpars,MOM-method", "SubCpars,OM-method" ] }, { "page": "SubOM", "title": "Subset a Stock, Fleet, Obs, or Imp object from an OM object", "topics": [ "SubOM" ] }, { "page": "Subset", "title": "Subset an object by simulation, year, age, MP, and/or fleet", "topics": [ "Subset" ] }, { "page": "summary-Data", "title": "Summary of Data object", "topics": [ "summary,Data-method" ] }, { "page": "summary-MMSE", "title": "Summary of MMSE object", "topics": [ "summary,MMSE-method" ] }, { "page": "summary-MSE", "title": "Summary of MSE object", "topics": [ "summary,MSE-method" ] }, { "page": "SumOverDim", "title": "Sum over named array dimensions", "topics": [ "SumOverAge", "SumOverArea", "SumOverClass", "SumOverFleet", "SumOverStock", "SumOverYear" ] }, { "page": "TAC", "title": "Calculate TAC recommendations for more than one MP", "topics": [ "TAC" ] }, { "page": "TACfilter", "title": "TAC Filter", "topics": [ "TACfilter" ] }, { "page": "TACs", "title": "Extract TAC Recommendations from an MSE Object", "topics": [ "TACs" ] }, { "page": "Taxa_Table", "title": "Taxa_Table", "topics": [ "Taxa_Table" ] }, { "page": "TEG", "title": "Tom's expand grid", "topics": [ "TEG" ] }, { "page": "OM-class-objects", "title": "OM class objects", "topics": [ "OM-class-objects", "testOM" ] }, { "page": "Thresh_tab", "title": "Current default thresholds for DFO satisficing", "topics": [ "Thresh_tab" ] }, { "page": "timeseries-class", "title": "'Timeseries' Class", "topics": [ "timeseries-class" ] }, { "page": "tinyErr", "title": "Remove observation, implementation, and process error", "topics": [ "tinyErr", "tinyErr,OM-method" ] }, { "page": "TradePlot", "title": "Generic Trade-Plot Function", "topics": [ "NOAA_plot2", "Tplot", "Tplot2", "Tplot3", "TradePlot" ] }, { "page": "tune_MP", "title": "Tune MP", "topics": [ "tune_MP" ] }, { "page": "Turing", "title": "Turing Test", "topics": [ "Turing", "TuringMOM" ] }, { "page": 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"topics": [ "VOI2" ] }, { "page": "VOIplot", "title": "Yet another Value of Information Plot", "topics": [ "VOIplot" ] }, { "page": "Weight", "title": "Weight Constructor and Accessors", "concept": [ "weight" ], "topics": [ "AWK", "AWK<-", "Weight", "Weight<-" ] }, { "page": "weight-class", "title": "The 'weight' S4 Class", "concept": [ "weight" ], "topics": [ "weight-class" ] }, { "page": "Weight-Models", "title": "Weight-at-Age and Weight-at-Length Models", "topics": [ "Weight-Models", "WeightatAge", "WeightatLength", "WeightatMeanLength", "WeightModels" ] }, { "page": "WHAM2OM", "title": "Takes a fitted SAM model and samples historical population and fishing dynamics from the MLE fit and variance-covariance matrix.", "topics": [ "WHAM2OM" ] }, { "page": "wormplot", "title": "Biomass wormplot", "topics": [ "wormplot" ] }, { "page": "WrappedNormal", "title": "Wrapped Normal Distribution", "topics": [ "WrappedNormal" ] }, { "page": "writeCSV", "title": "Internal function to write CSVs 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