Man pages for StoXProject/RstoxFDA
Fisheries Dependent Analysis with RstoX
| activityCensus | Activity census |
| AddAreaPositionStoxLanding | Append position to landings data |
| AddGearGroupStoxBiotic | Add Gear group to StoxBioticData |
| AddGearGroupStoxLanding | Add Gear group to StoxLandingData |
| addLogbookColumns | Add columns from logbooks |
| AddPeriodStoxBiotic | Add Period to StoxBioticData |
| AddPeriodStoxLanding | Add Period to StoxLandingData |
| AddStratumStoxBiotic | Adds Stratum to StoxBioticData |
| AddStratumStoxLanding | Adds Strata to StoxLandingData |
| AgeErrorMatrix | Age Error Matrix (AgeErrorMatrix) |
| AnalyticalPopulationEstimateData | Analytical Population Estimate Data |
| AnalyticalPSUEstimateData | Analytical PSU Estimate Data |
| appendAreaCode | Append area code |
| appendMetier | Annotate metier |
| appendPosition | Append positions |
| appendTripIdLandings | Assign trip IDs |
| appendTripIdLogbooks | Assing trip ID to logbooks |
| areaCodeConversionTable | Make area code conversion table |
| AreaPosition | Area Code Positions (AreaPosition) |
| calculateLogbookPartitionByTrip | Calcualte catch partition |
| CarNeighbours | Area Neighbour Definition (CarNeighbours) |
| CatchLotteryExample | Data from the Norwegian catch lottery sampling program. |
| CatchLotteryLandingExample | Landings for the Norwegian North Sea Herring fisheries in... |
| CatchLotterySamplingExample | Sampling parameters from the Norwegian catch lottery sampling... |
| catchsamples | Data from Norwegian port sampling program. |
| categoriseDate | Get temporal categories |
| convertCodes | Convert codes. |
| ConvertLengthBiotic | Convert lengths Biotic |
| convertRecaData | Convert RecaData |
| convertToErsData | Convert logbook data |
| ConvertWeightBiotic | Convert weights Biotic |
| DefineAgeErrorMatrix | Define Age Error Matrix |
| DefineAreaPosition | Define Area Code Positions |
| DefineCarNeighbours | Define CAR neighbours |
| DefineLengthConversionParameters | Define Length Conversion Parameters |
| DefinePeriod | Define Periods |
| DefineStockSplittingParameters | Define Stock Splitting Parameters |
| DefineWeightConversionFactor | Define Weight Conversion Factors |
| FDIR.factors.VIII.2022 | Weigh conversion Factors (FDIR VIII, 2022) |
| FilterAgeLengthOutliersStoxBiotic | Filter outliers |
| filterLogLinear | Filter length-weight outliers |
| filterVonBsigma | Filter length-age outliers |
| FilterWeightLengthOutliersStoxBiotic | Filter length-weight outliers |
| GearGroupFdirTable | Gear groups |
| getCovariateMap | Make Covariate Map |
| getLandings | Formats landings for R-ECA. |
| GSAsubArea | GFCM sub areas (mixed area codes) |
| ICESareas | ICES areas (mixed area codes from 2018) |
| ICESdivision | ICES Divisions (area codes from 2018) |
| ICESrectangles | ICES rectangles |
| ICESsubArea | ICES sub-areas (area codes from 2018) |
| ICESsubDivision | ICES sub-divisions (area codes from 2018) |
| ICESunit | ICES units (area codes) |
| imputeCatchesLandings | Impute catches to landings |
| IndividualSamplingParametersData | Individual Sub-Sampling Design Parameters |
| is.AgeErrorMatrix | Check if argument is AgeErrorMatrix |
| is.AreaPosition | Check if argument is AreaPosition |
| is.CarNeighbours | Check if argument is CarNeighbours |
| is.LengthConversionTable | Check if argument is LengthConversionTable |
| is.ParameterConvergenceData | Checks if argument is 'ParameterConvergenceData' |
| is.ParameterizationSummaryData | Checks if argument is 'ParameterizationSummaryData' |
| is.RecaCatchAtAge | Check if argument is RecaCatchAtAge |
| is.RecaData | Check if argument is RecaData |
| is.RecaParameterData | Check if argument is RecaParameterData |
| is.RecaResult | Check if argument is RecaResult |
| is.ReportFdaData | Checks if argument is 'ReportFdaData' |
| is.ReportFdaSamplingData | Check if argument is ReportFdaSamplingData |
| is.ReportFdaSOP | Checks if argument is 'ReportFdaSOP' |
| is.StockSplittingParameters | Check if argument is StockSplittingParameters |
| is.TemporalDefinition | Check if argument is TemporalDefinition |
| is.Translation | Checks if argument is 'Translation' |
| is.WeightConversionTable | Check if argument is WeightConversionTable |
| KommunePolygons | Kommune polygons |
| kommuner2022 | Norwegian municipalities (kommune) |
| LandingData | Landing data (LandingData) |
| landings | Landings of Haddock |
| LandingsArchiveData | Landings archive (LandingsArchiveData) |
| LengthConversionTable | Length Conversion Table (LengthConversionTable) |
| ListBioticDifference | List Difference |
| LoadFdaStratumPolygon | Load common area definitions |
| locationsFdir2017 | Location codes (FDIR to 2017 incl.) |
| locationsFdir2018 | Location codes (FDIR from 2018 incl.) |
| LocodeTable | LOCODE table (LocodeTable) |
| logbookAdjustment | Adjust landings by logbooks |
| LstLogbookData | Logbooks (LstLogbookData) |
| mainareaFdir2017 | Main areas (FDIR to 2017 incl.) |
| mainareaFdir2018 | Main areas (FDIR from 2018 incl.) |
| makeAgeTracesRECA | Catch at age traces |
| makeResultTableRECA | Catch at Age result table |
| makeTripIds | Make trip IDs |
| mergePolygons | Merges polygons |
| metier4table | MetierTable lvl 4 example |
| metier5table | MetierTable lvl 5 example |
| metier6table | MetierTable lvl 6 example |
| MetierTable | Metier table |
| NAFOareas | NAFO areas |
| ParameterConvergenceData | Convergence Report for simulated parameters... |
| ParameterizationSummaryData | Summary statistics for simulated parameters... |
| ParameterizeRecaModels | Parameterize Reca. |
| plotAgeTraces | Traceplot |
| plotArea | Plot area definitions on a map |
| plotAreaComparison | Compare area definitions |
| plotBubbleMap | Plots bubble plot on map |
| plotCatchAtAge | Catch at Age plot |
| PlotCatchAtAgeTotals | Plot Catch At Age |
| PlotCatchAtAgeTotalsData | Total catch by age plot (PlotCatchAtAgeTotalsData) |
| PlotFisheriesOverviewSpatial | Plot spatial distribution of fisheries |
| PlotFisheriesOverviewSpatialData | Spatial landings overview data... |
| PlotFisheriesOverviewTemporal | Plot landings |
| PlotFisheriesOverviewTemporalData | Temporal landings overview data... |
| PlotMeanLengthAtAge | Plot length at age |
| PlotMeanLengthAtAgeData | Mean length at age plot (PlotMeanLengthAtAgeData) |
| PlotMeanWeightAtAge | Plot weight at age |
| PlotMeanWeightAtAgeData | Mean weight at age plot (PlotMeanWeightAtAgeData) |
| PlotPosteriorTraces | Reca Traceplots |
| PlotPosteriorTracesData | Trace plot (PlotPosteriorTracesData) |
| PlotSamplingCoverage | Coverage plot |
| PlotSamplingCoverageData | Sampling variables plot data (PlotSamplingCoverageData) |
| PlotSamplingOverviewCell | Cell plot |
| PlotSamplingOverviewCellData | Sampling Overview cell-plot data... |
| PlotSamplingVariables | Plot sampling variables |
| PlotSamplingVariablesData | Sampling variables plot data (PlotSamplingVariablesData) |
| portcodes2020 | UN Location codes for ports |
| PrepareRecaEstimate | Prepare data for Reca. |
| prepRECA | Prepare data for R-ECA |
| processPropertyFormats | Define the process property formats for inclusion in stox UI |
| PSUSamplingParametersData | PSU Sampling Design Parameters |
| readFdirLandingsArchive | Reads landings archive |
| ReadLandingFDA | Read landing files |
| readLstFile | Parses logbooks (lst) |
| readMetierTable | Read metier table |
| RecaCatchAtAge | Reca Results (RecaCatchAtAge) |
| RecaCatchAtAgeExample | Saithe landings 2021. |
| RecaData | Reca Data (RecaData) |
| recaDataExample | Example data for Reca |
| rEcaDataReport | Data report for R-ECA preparation |
| RecaParameterData | Reca Parameter Data (RecaParameterData) |
| recaPrediction | Example result from Reca |
| RecaResult | Reca Results (RecaResult) |
| ReportFdaCatchAtAgeCovarianceData | Fisheries dependent Catch At Age Covariance Report... |
| ReportFdaCatchAtAgeData | Fisheries dependent Catch At Age Report... |
| ReportFdaCatchAtLengthAndAgeData | Fisheries dependent Catch At Age Report... |
| ReportFdaCatchAtLengthData | Fisheries dependent Catch At Age Report... |
| ReportFdaData | Age group statistics (ReportFdaData) |
| ReportFdaLandingData | Landings Report data (ReportFdaLandingData) |
| ReportFdaLandings | Report FDA landings |
| ReportFdaLengthAtAgeData | Fisheries dependent Length At Age Report... |
| ReportFdaSampling | Report FDA sampling |
| ReportFdaSamplingData | Sampling Report data (ReportFdaSamplingData) |
| ReportFdaSOP | Report SOP test |
| ReportFdaSopData | Sum of Products report (ReportFdaSopData) |
| ReportFdaSummaryData | Total catch statistics (ReportFdaSummaryData) |
| ReportFdaWeightAtAgeData | Reca Weight At Age Report (ReportFdaWeightAtAgeData) |
| ReportParameterConvergence | Report convergence Statistics for parameter simulations |
| ReportRecaCatchAtAge | Report catch at age |
| ReportRecaCatchAtAgeCovariance | Report covariance of catch at age |
| ReportRecaCatchAtLength | Report catch at length |
| ReportRecaCatchAtLengthAndAge | Report catch at length and age |
| ReportRecaCatchStatistics | Report catch statistics |
| ReportRecaLengthAtAge | Report length at age |
| ReportRecaParameterStatistics | Report summary statistics for Reca paramters |
| ReportRecaWeightAtAge | Report weight at age |
| RstoxFDA | Fisheries Dependent Analysis with RstoX |
| runRECA | Run R-ECA |
| RunRecaEstimate | Run Reca. |
| RunRecaModels | Run Reca Models |
| sanitizeRecaInput | Input sanitation for Reca |
| SetAreaPositionsBiotic | Set position Biotic |
| SetShortGearBiotic | Set short gear codes biotic |
| SetStartDateBiotic | Set startdate Biotic |
| SetTimeBiotic | Set time Biotic |
| sourceLogbookColumns | Fill in values from logbooks |
| StockSplittingParameters | Stock splitting parameters (StockSplittingParameters) |
| StoxBioticDataExample | Data from Norwegian port sampling program. |
| stoxFunctionAttributes | Function specification for inclusion in StoX UI |
| StoxLandingDataExample | Saithe landings 2021. |
| tabulateFisheries | Tabulate fisheries |
| TemporalDefinition | Temporal Categories (TemporalDefinition) |
| TripPartition | Trip Partition |
| WeightConversionTable | Weight Conversion Table (WeightConversionTable) |
| writeSpDataFrameAsWKT | Writes shape files as WKT files |
