Package index • RstoxFDA

StoX-functions

Functions that are available in the StoX user interface. These are otherwise identified by their names starting with a capital letter

AddAreaPositionStoxLanding(): Append position to landings data

AddGearGroupStoxBiotic(): Add Gear group to StoxBioticData

AddGearGroupStoxLanding(): Add Gear group to StoxLandingData

AddPeriodStoxBiotic(): Add Period to StoxBioticData

AddPeriodStoxLanding(): Add Period to StoxLandingData

AddPsuStratificationVariables(): Add Stratification columns to 'PSUSamplingParametersData'

AddStratumStoxBiotic(): Adds Stratum to StoxBioticData

AddStratumStoxLanding(): Adds Strata to StoxLandingData

AssignPSUSamplingParameters(): Assign PSU Sampling Parameters

ComputeIndividualSamplingParameters(): Compute Sampling Parameters for Individuals

ComputePSUSamplingParameters(): Compute PSU Sampling Design Parameters

ConvertLengthBiotic(): Convert lengths Biotic

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

FilterAgeLengthOutliersStoxBiotic(): Filter outliers

FilterWeightLengthOutliersStoxBiotic(): Filter length-weight outliers

ListBioticDifference(): List Difference

LoadFdaStratumPolygon(): Load common area definitions

ParameterizeRecaModels(): Parameterize Reca.

PlotCatchAtAgeTotals(): Plot Catch At Age

PlotFisheriesOverviewSpatial(): Plot spatial distribution of fisheries

PlotFisheriesOverviewTemporal(): Plot landings

PlotMeanLengthAtAge(): Plot length at age

PlotMeanWeightAtAge(): Plot weight at age

PlotPosteriorTraces(): Reca Traceplots

PlotSamplingCoverage(): Coverage plot

PlotSamplingOverviewCell(): Cell plot

PlotSamplingVariables(): Plot sampling variables

PrepareRecaEstimate(): Prepare data for Reca.

ReadLandingFDA(): Read landing files

ReadPSUSamplingParameters(): Read PSU Sampling Design Parameters

ReportAnalyticalCatchAtAge(): Report catch at age

ReportAnalyticalCatchAtLength(): Report catch at length

ReportAnalyticalLengthAtAge(): Report mean length at age

ReportAnalyticalWeightAtAge(): Report mean weight at age

ReportFdaLandings(): Report FDA landings

ReportFdaSOP(): Report SOP test

ReportFdaSampling(): Report FDA sampling

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

RunRecaModels(): Run Reca Models

SetAreaPositionsBiotic(): Set position Biotic

SetShortGearBiotic(): Set short gear codes biotic

SetStartDateBiotic(): Set startdate Biotic

Spatial coding functions

Functions for encoding and re-coding spatial information

AddAreaPositionStoxLanding(): Append position to landings data

AddStratumStoxBiotic(): Adds Stratum to StoxBioticData

AddStratumStoxLanding(): Adds Strata to StoxLandingData

DefineAreaPosition(): Define Area Code Positions

DefineCarNeighbours(): Define CAR neighbours

LoadFdaStratumPolygon(): Load common area definitions

SetAreaPositionsBiotic(): Set position Biotic

appendAreaCode(): Append area code

appendPosition(): Append positions

areaCodeConversionTable(): Make area code conversion table

convertCodes(): Convert codes.

mergePolygons(): Merges polygons

plotArea(): Plot area definitions on a map

plotAreaComparison(): Compare area definitions

writeSpDataFrameAsWKT(): Writes shape files as WKT files

Spatial coding systems

Polygons defining area coding systems

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)

NAFOareas: NAFO areas

kommuner2022: Norwegian municipalities (kommune)

locationsFdir2017: Location codes (FDIR to 2017 incl.)

locationsFdir2018: Location codes (FDIR from 2018 incl.)

mainareaFdir2017: Main areas (FDIR to 2017 incl.)

mainareaFdir2018: Main areas (FDIR from 2018 incl.)

portcodes2020: UN Location codes for ports

Temporal coding functions

Functions for encoding and re-coding temporal information

AddPeriodStoxBiotic(): Add Period to StoxBioticData

AddPeriodStoxLanding(): Add Period to StoxLandingData

DefinePeriod(): Define Periods

SetStartDateBiotic(): Set startdate Biotic

categoriseDate(): Get temporal categories

convertCodes(): Convert codes.

Gear coding functions

Functions and example data for encoding and re-coding gear information

AddGearGroupStoxBiotic(): Add Gear group to StoxBioticData

AddGearGroupStoxLanding(): Add Gear group to StoxLandingData

GearGroupFdirTable: Gear groups

SetShortGearBiotic(): Set short gear codes biotic

appendMetier(): Annotate metier

convertCodes(): Convert codes.

metier4table: MetierTable lvl 4 example

metier5table: MetierTable lvl 5 example

metier6table: MetierTable lvl 6 example

readMetierTable(): Read metier table

Parameter conversion functions

Functions and data for converting bilogical parameters

ConvertLengthBiotic(): Convert lengths Biotic

ConvertWeightBiotic(): Convert weights Biotic

DefineLengthConversionParameters(): Define Length Conversion Parameters

DefineWeightConversionFactor(): Define Weight Conversion Factors

FDIR.factors.VIII.2022: Weigh conversion Factors (FDIR VIII, 2022)

Landing functions

Functions and example data for handling landings data (sales-notes etc.)

PlotFisheriesOverviewSpatial(): Plot spatial distribution of fisheries

PlotFisheriesOverviewTemporal(): Plot landings

PlotSamplingCoverage(): Coverage plot

PlotSamplingOverviewCell(): Cell plot

PlotSamplingVariables(): Plot sampling variables

ReadLandingFDA(): Read landing files

ReportFdaLandings(): Report FDA landings

ReportFdaSampling(): Report FDA sampling

addLogbookColumns(): Add columns from logbooks

appendTripIdLandings(): Assign trip IDs

imputeCatchesLandings(): Impute catches to landings

landings: Landings of Haddock

logbookAdjustment(): Adjust landings by logbooks

makeTripIds(): Make trip IDs

plotBubbleMap(): Plots bubble plot on map

sourceLogbookColumns(): Fill in values from logbooks

tabulateFisheries(): Tabulate fisheries

Logbook functions

Functions and example data for handling logbook data from fisheries

activityCensus: Activity census

addLogbookColumns(): Add columns from logbooks

appendTripIdLandings(): Assign trip IDs

appendTripIdLogbooks(): Assing trip ID to logbooks

calculateLogbookPartitionByTrip(): Calcualte catch partition

convertToErsData(): Convert logbook data

imputeCatchesLandings(): Impute catches to landings

logbookAdjustment(): Adjust landings by logbooks

makeTripIds(): Make trip IDs

readLstFile(): Parses logbooks (lst)

sourceLogbookColumns(): Fill in values from logbooks

IO functions

Functions for reading or writing data files, or converting data formats

ReadLandingFDA(): Read landing files

convertToErsData(): Convert logbook data

readFdirLandingsArchive(): Reads landings archive

readLstFile(): Parses logbooks (lst)

NMDbiotic functions

Functions for Biotic-data in StoX that assumes NMDbiotic as data source

ConvertLengthBiotic(): Convert lengths Biotic

ConvertWeightBiotic(): Convert weights Biotic

ListBioticDifference(): List Difference

SetAreaPositionsBiotic(): Set position Biotic

SetShortGearBiotic(): Set short gear codes biotic

SetStartDateBiotic(): Set startdate Biotic

Data QA functions

Functions for quality checking data

FilterAgeLengthOutliersStoxBiotic(): Filter outliers

FilterWeightLengthOutliersStoxBiotic(): Filter length-weight outliers

ListBioticDifference(): List Difference

ReportFdaSOP(): Report SOP test

filterLogLinear(): Filter length-weight outliers

filterVonBsigma(): Filter length-age outliers

StoX-Reca functions

StoX-functions preparing data for and running Reca

AddStratumStoxLanding(): Adds Strata to StoxLandingData

DefineAgeErrorMatrix(): Define Age Error Matrix

DefineStockSplittingParameters(): Define Stock Splitting Parameters

ParameterizeRecaModels(): Parameterize Reca.

PlotFisheriesOverviewSpatial(): Plot spatial distribution of fisheries

PlotFisheriesOverviewTemporal(): Plot landings

PlotSamplingCoverage(): Coverage plot

PlotSamplingOverviewCell(): Cell plot

PlotSamplingVariables(): Plot sampling variables

PrepareRecaEstimate(): Prepare data for Reca.

RecaCatchAtAgeExample: Saithe landings 2021.

ReportAnalyticalCatchAtAge(): Report catch at age

ReportAnalyticalCatchAtLength(): Report catch at length

ReportAnalyticalLengthAtAge(): Report mean length at age

ReportAnalyticalWeightAtAge(): Report mean weight at age

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

RunRecaModels(): Run Reca Models

StoxBioticDataExample: Data from Norwegian port sampling program.

StoxLandingDataExample: Saithe landings 2021.

Convergence check functions

Functions for checking convergence of Reca models.

PlotMeanLengthAtAge(): Plot length at age

PlotMeanWeightAtAge(): Plot weight at age

PlotPosteriorTraces(): Reca Traceplots

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

catchsamples: Data from Norwegian port sampling program.

convertRecaData(): Convert RecaData

getCovariateMap(): Make Covariate Map

getLandings(): Formats landings for R-ECA.

landings: Landings of Haddock

makeAgeTracesRECA(): Catch at age traces

makeResultTableRECA(): Catch at Age result table

plotAgeTraces(): Traceplot

plotCatchAtAge(): Catch at Age plot

prepRECA(): Prepare data for R-ECA

rEcaDataReport(): Data report for R-ECA preparation

recaDataExample: Example data for Reca

recaPrediction: Example result from Reca

runRECA(): Run R-ECA

sanitizeRecaInput(): Input sanitation for Reca

tabulateFisheries(): Tabulate fisheries

Other functions and data

RstoxFDA functions and data not mentioned elsewhere

AddAreaPositionStoxLanding(): Append position to landings data

AddLengthGroupStoxBiotic(): Add length group to StoxBioticData

AddStratumStoxBiotic(): Adds Stratum to StoxBioticData

AggregateAnalyticalEstimate(): Aggregate Analytical Estimate across strata

AnalyticalPSUEstimate(): Estimate parameters for each Primary Sampling Unit

AnalyticalPSUEstimateData: Analytical PSU Estimate Data

AnalyticalPopulationEstimate(): Analytical estimate of population parameters

AnalyticalPopulationEstimateData: Analytical Population Estimate Data

AnalyticalRatioEstimate(): Ratio estimate to census landings

CatchLotteryExample: Data from the Norwegian catch lottery sampling program.

CatchLotteryLandingExample: Landings for the Norwegian North Sea Herring fisheries in 2022.

CatchLotterySamplingExample: Sampling parameters from the Norwegian catch lottery sampling program.

CollapseStrata(): Collapse strata in sampling design

ConvertLengthBiotic(): Convert lengths Biotic

ConvertWeightBiotic(): Convert weights Biotic

DefineAreaPosition(): Define Area Code Positions

DefineCarNeighbours(): Define CAR neighbours

ExtendAnalyticalSamplingFrameCoverage(): Extends estimate beyond sampling frame

FilterAgeLengthOutliersStoxBiotic(): Filter outliers

FilterWeightLengthOutliersStoxBiotic(): Filter length-weight outliers

IndividualSamplingParametersData: Individual Sub-Sampling Design Parameters

InterpolateAnalyticalDomainEstimates(): Interpolate means and frequencies for zero-abundance domains

LiftStrata(): Unify strata for AnalyticalPSUEstimateData

LoadFdaStratumPolygon(): Load common area definitions

PSUSamplingParametersData: PSU Sampling Design Parameters

PlotFisheriesOverviewSpatial(): Plot spatial distribution of fisheries

PlotFisheriesOverviewTemporal(): Plot landings

PlotMeanLengthAtAge(): Plot length at age

PlotMeanWeightAtAge(): Plot weight at age

PlotPosteriorTraces(): Reca Traceplots

PlotSamplingCoverage(): Coverage plot

PlotSamplingOverviewCell(): Cell plot

PlotSamplingVariables(): Plot sampling variables

ReadLandingFDA(): Read landing files

ReportFdaLandings(): Report FDA landings

ReportFdaSOP(): Report SOP test

ReportFdaSampling(): Report FDA sampling

ReportParameterConvergence(): Report convergence Statistics for parameter simulations

ReportRecaParameterStatistics(): Report summary statistics for Reca paramters

RstoxFDA: Fisheries Dependent Analysis with RstoX

SetStartDateBiotic(): Set startdate Biotic

convertToErsData(): Convert logbook data

landings: Landings of Haddock

processPropertyFormats: Define the process property formats for inclusion in stox UI

readLstFile(): Parses logbooks (lst)

stoxFunctionAttributes: Function specification for inclusion in StoX UI

tabulateFisheries(): Tabulate fisheries

Data types

Data types and functions for asserting the validity of data types

AgeErrorMatrix: Age Error Matrix (AgeErrorMatrix)

AnalyticalPSUEstimateData: Analytical PSU Estimate Data

AnalyticalPopulationEstimateData: Analytical Population Estimate Data

AreaPosition: Area Code Positions (AreaPosition)

CarNeighbours: Area Neighbour Definition (CarNeighbours)

IndividualSamplingParametersData: Individual Sub-Sampling Design Parameters

KommunePolygons: Kommune polygons

LandingData: Landing data (LandingData)

LandingsArchiveData: Landings archive (LandingsArchiveData)

LengthConversionTable: Length Conversion Table (LengthConversionTable)

LocodeTable: LOCODE table (LocodeTable)

LstLogbookData: Logbooks (LstLogbookData)

MetierTable: Metier table

PSUSamplingParametersData: PSU Sampling Design Parameters

ParameterConvergenceData: Convergence Report for simulated parameters (ParameterConvergenceData)

ParameterizationSummaryData: Summary statistics for simulated parameters (ParameterizationSummaryData)

PlotCatchAtAgeTotalsData: Total catch by age plot (PlotCatchAtAgeTotalsData)

PlotFisheriesOverviewSpatialData: Spatial landings overview data (PlotFisheriesOverviewSpatialData)

PlotFisheriesOverviewTemporalData: Temporal landings overview data (PlotFisheriesOverviewTemporalData)

PlotMeanLengthAtAgeData: Mean length at age plot (PlotMeanLengthAtAgeData)

PlotMeanWeightAtAgeData: Mean weight at age plot (PlotMeanWeightAtAgeData)

PlotPosteriorTracesData: Trace plot (PlotPosteriorTracesData)

PlotSamplingCoverageData: Sampling variables plot data (PlotSamplingCoverageData)

PlotSamplingOverviewCellData: Sampling Overview cell-plot data (PlotSamplingOverviewCellData)

PlotSamplingVariablesData: Sampling variables plot data (PlotSamplingVariablesData)

RecaCatchAtAge: Reca Results (RecaCatchAtAge)

RecaData: Reca Data (RecaData)

RecaParameterData: Reca Parameter Data (RecaParameterData)

RecaResult: Reca Results (RecaResult)

ReportFdaCatchAtAgeCovarianceData: Fisheries dependent Catch At Age Covariance Report (ReportFdaCatchAtAgeCovarianceData)

ReportFdaCatchAtAgeData: Fisheries dependent Catch At Age Report (ReportFdaCatchAtAgeData)

ReportFdaCatchAtLengthAndAgeData: Fisheries dependent Catch At Age Report (ReportFdaCatchAtLengthAndAgeData)

ReportFdaCatchAtLengthData: Fisheries dependent Catch At Age Report (ReportFdaCatchAtLengthData)

ReportFdaData: Age group statistics (ReportFdaData)

ReportFdaLandingData: Landings Report data (ReportFdaLandingData)

ReportFdaLengthAtAgeData: Fisheries dependent Length At Age Report (ReportFdaLengthAtAgeData)

ReportFdaSamplingData: Sampling Report data (ReportFdaSamplingData)

ReportFdaSopData: Sum of Products report (ReportFdaSopData)

ReportFdaSummaryData: Total catch statistics (ReportFdaSummaryData)

ReportFdaWeightAtAgeData: Reca Weight At Age Report (ReportFdaWeightAtAgeData)

StockSplittingParameters: Stock splitting parameters (StockSplittingParameters)

TemporalDefinition: Temporal Categories (TemporalDefinition)

TripPartition: Trip Partition

WeightConversionTable: Weight Conversion Table (WeightConversionTable)

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.ReportFdaSOP(): Checks if argument is ReportFdaSOP

is.ReportFdaSamplingData(): Check if argument is ReportFdaSamplingData

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

Deprecated functions

Functions that are candidates for removal from RstoxData in future releases. Their help pages suggest alterntive functions to use in stead.

RunRecaEstimate(): Run Reca.

SetTimeBiotic(): Set time Biotic