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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
AddStratumStoxBiotic()
Adds Stratum to StoxBioticData
AddStratumStoxLanding()
Adds Strata to StoxLandingData
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
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.
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

RstoxFDA RstoxFDA-package
Fisheries Dependent Analysis with RstoX
processPropertyFormats
Define the process property formats for inclusion in stox UI
stoxFunctionAttributes
Function specification for inclusion in StoX UI

Data types

Data types and functions for asserting the validity of data types

AgeErrorMatrix
Age Error Matrix (AgeErrorMatrix)
AreaPosition
Area Code Positions (AreaPosition)
CarNeighbours
Area Neighbour Definition (CarNeighbours)
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
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