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