Package index • RstoxBase

All functions
`AcousticDensity()`	Calculate number density from NASC in length intervals
`AcousticLayer`	Acoustic Layer
`AcousticPSU`	Acoustic PSU
`AcousticTargetStrength`	Acoustic target strength
`AddHaulDensityToSuperIndividuals()`	Add haul density to SuperIndividualsData
`AddPSUToPreySpeciesCategoryCatch()`	Add Survey, Stratum and PSU to PreySpeciesCategoryCatchData
`AppendNASC()`	Append to NASCData
`AssignmentLengthDistribution()`	Assignment length distribution per acoustic PSU
`AssignmentLengthDistributionData`	Assignment length distribution data
`BioticAssignment`	Biotic assignment
`BioticAssignmentWeighting()`	Weighting of biotic hauls in biotic assignment
`BioticLayer`	Biotic Layer
`BioticPSU`	Biotic PSU
`Channel`	Input vertical resolution for acoustic-trawl models
`DataTypes`	StoX data types of the RstoxBase package
`DefineAcousticLayer()`	Define Acoustic Layer
`DefineAcousticPSU()`	Acoustic PSU
`DefineAcousticTargetStrength()`	Acoustic target strength definition
`DefineBioticAssignment()`	Assignment of biotic hauls to acoustic PSUs by layer
`DefineBioticLayer()`	Define biotic Layer
`DefineBioticPSU()`	Biotic PSU
`DefineLayer()`	Define Layers
`DefineModel()`	Define a parametric or numeric model
`DefinePSU()`	Define PSU
`DefineRegression()`	Define a regression model and parameters
`DefineStratumPolygon()`	Define stratum multipolygon
`DefineSurvey()`	Define Survey
`DensityData`	Density data
`EDSU`	Horizontal input resolution for acoustic-trawl models
`EstimateBioticRegression()`	Estimate a regression model and parameters for biotic data
`GearDependentCatchCompensation()`	Apply the sweep of different gear (and cruise)
`GearDependentLengthDistributionCompensation()`	Apply the sweep of different gear (and cruise)
`GearDependentSpeciesCategoryCatchCompensation()`	Apply the sweep of different gear (and cruise)
`Haul`	Input vertical resolution for swept-area models
`ImputeSuperIndividuals()`	Impute missing super-individual data
`ImputeSuperIndividuals_StoX3()`	Impute missing super-individual data
`Individuals()`	Indivduals to distribute abundance to to create super-individuals
`IndividualsData`	Individuals data
`Layer`	Layer vertical resolution
`LengthDependentLengthDistributionCompensation()`	Catchability of trawls by fish length
`LengthDistribution()`	Length distribution
`LengthDistributionData`	Length distribution data
`MeanDensity()`	Mean density in each stratum
`MeanDensityData`	Mean density data
`MeanLengthDistribution()`	Mean length distribution over Stations in each AcousticPSU
`MeanLengthDistributionData`	Mean length distribution data
`MeanNASC()`	Mean NASC
`MeanNASCData`	Mean NASC data
`MeanSpeciesCategoryCatch()`	Mean species category catch over Stations in each AcousticPSU
`MeanSpeciesCategoryCatchData`	Total catch per SpeciesCategory and biotic PSU
`ModelData`	Model data used by RstoxBase
`NASC()`	NASC
`NASCData`	Nautical area scattering coefficient (NASC) data
`NASCToStoxAcoustic()`	Convert NASCData to StoxAcousticData
`PSU`	Acoustic and biotic primary sampling units
`PlotAcousticTrawlSurvey()`	Plot NASCData
`PlotAcousticTrawlSurveyData`	Plot Acoustic-Trawl Survey data
`PreySpeciesCategoryCatch()`	Table of total catch weight and number per Haul and SpeciesCategory
`PreySpeciesCategoryCatchData`	Total prey catch per PreySpeciesCategory and Individual
`ProcessData`	Process data used by RstoxBase
`Quantity()`	Calculate abundance in the strata
`QuantityData`	Quantity data
`Regression`	Regression
`RegroupLengthDistribution()`	Regroup length distribution to common intervals
`RelativeLengthDistribution()`	Relative length distribution
`ReportDensity()`	Report DensityData
`ReportDensityData`	Reported Density data
`ReportFunctions`	Report functions for baseline process output
`ReportPreySpeciesCategoryCatch()`	Report PreySpeciesCategoryCatchData
`ReportPreySpeciesCategoryCatchData`	Reported PreySpeciesCategoryCatch data
`ReportQuantity()`	Report QuantityData
`ReportQuantityData`	Reported Quantity data
`ReportSpeciesCategoryCatch()`	Report SpeciesCategoryCatch
`ReportSpeciesCategoryCatchData`	Reported SpeciesCategoryCatch data
`ReportSuperIndividuals()`	Report SuperIndividualsData
`ReportSuperIndividualsData`	Reported super-individuals data
`Resolution`	Resolution
`RstoxBase-package` `RstoxBase`	Base StoX Functions
`SpeciesCategoryCatch()`	Table of total catch weight and number per Haul and SpeciesCategory
`SpeciesCategoryCatchData`	Total catch per SpeciesCategory and Haul
`SplitMeanNASC()`	Split MeanNASCData to NASCData (deprecated)
`SplitNASC()`	Split NASCData
`Station`	Horizontal input resolution for swept-area models
`StoX_multipolygon_WKT`	StoX multipolygon WKT
`StoxDataStartMiddleStopDateTime()`	Generate Start, Middle and Stop DateTime variables
`Stratum`	Stratum horizontal resolution
`StratumArea()`	Calculate area of each stratum
`StratumAreaData`	Stratum area data
`StratumPolygon`	StoX data type StratumPolygon
`SumLengthDistribution()`	Sum length distribution vertically over Hauls of each Station
`SumLengthDistributionData`	Summed length distribution data
`SumNASC()`	Sum NASC
`SumNASCData`	Summed NASC data
`SumSpeciesCategoryCatch()`	Sum species category catch over Hauls for each Station
`SumSpeciesCategoryCatchData`	Total catch per SpeciesCategory and Station
`SuperIndividuals()`	Super-indivduals with abundance
`SuperIndividualsData`	Super-individuals data
`Survey`	StoX data type Survey
`SweptAreaDensity()`	Swept-area density
`WriteStratumPolygon()`	Write StratumPolygon
`WriteStratumPolygonData`	Write StratumPolygon data
`aggregateBaselineDataOneTable()`	Function to aggregate baseline data
`aggregateBaselineDataOneTableSingleFunction()`	Function to aggregate baseline data
`allEqual()`	Test whether all values are equal.
`allargs()`	Get all arguments from inside a function
`backwardCompatibility_RstoxBase`	Backward compabitibility actions:
`combined.color()`	Combined rainbow and desaturation color scale
`cv()`	The coefficient of variation, i.e., the standard deviation divided by the mean.
`factorNAfirst()`	Convert to factor and put NAs first
`filterTable()`	Filter a table
`formatOutput()`	Function to format the output of a function returning StoX data (ModelData or ProcessData).
`formatProcessData()`	Format process data
`fractionOfOccurrence`	The fraction of occurrence function
`fractionOfSum`	The fraction of occurrence function
`general_arguments`	General parameters of RstoxBase
`general_arguments2.7`	General parameters of treating project.xml file from StoX <= 2.7
`general_map_plot_arguments`	General map plot parameters of RstoxBase
`general_plot_arguments`	General ploting parameters of RstoxBase
`general_report_arguments`	General report parameters of RstoxBase
`getBaseUnit()`	Get base unit of a variable of a StoX dataType
`getCommonIntervals()`	Get the common intervals of possibly overlapping intervals:
`getDataTypeDefinition()`	Get data type definitions
`getFunctionArgumentHierarchyForSpcificationParameters()`	Return a list of specification parameters with conditions for use in stoxFunctionAttributes
`getProjectXMLFilePath()`	Get the path to the project.xml file from StoX <= 2.7.
`getReportFunctionVariableName()`	Get the name of the target variable after aggregating.
`getReportFunctions()`	Function returning the report functions defined for reporting in StoX, such as sum, summaryStox, etc.
`getRstoxBaseDefinitions()`	Get RstoxBase definitions
`getSeedVector()`	Generate a seed vector consistently
`getStratumNames()` `addStratumNames()`	Extract or add stratum names from a SpatialPolygonsDataFrame
`hasBaseUnit()`	Does the variable of the StoX dataType have a base unit?
`modifyParameter_ProjectXMLList()`	Modify a parameter of a process of a list representation of a project.xml file from StoX <= 2.7.
`modifyProj4String()`	Define a proj4 string
`number()`	Number of TRUE
`processPropertyFormats`	Define the process property formats:
`readAcousticPSUFrom2.7()`	Read a the AcousticPSU from a project.xml file from StoX <= 2.7
`readBioticAssignmentFrom2.7()`	Read a the BioticAssignment from a project.xml file from StoX <= 2.7
`readBioticPSUFrom2.7()`	Read a the AcousticPSU from a project.xml file from StoX <= 2.7
`readProjectXMLToList()`	Read a project.xml file from StoX <= 2.7
`readStratumPolygonFrom2.7()` `writeStratumPolygonFrom2.7()`	Read a the StratumPolygon from a project.xml file from StoX <= 2.7
`renameSSULabelInPSUProcessData()`	Rename SSU to either EDSU or Station
`replaceNAByReference()`	Replace all NAs in a data.table by reference
`sampleSorted()`	Function to sample after sorting:
`setBaseUnit()`	Set base unit to a variable of the StoX dataType
`setDefaultsInStoxFunction()`	Set default general options
`setPlotAttributes()`	Set plot attributes to a plot object
`setUnitRstoxBase()`	Set units to a variable of the StoX dataType
`stoxFunctionAttributes`	A list of the attributes of the exported StoX functions: The format describes the actual content, such as catchabilityTable, filePath, filter, etc. These are used by StoX to choose action on these parameters. The primitive type (one of integer, double, logical, character) will be interpreted in the process property functions from the type of the function input or parameter.
`summaryStox()`	The summary function introduced in StoX <= 2.7.
`toJSON_Rstox()`	Convert to JSON
`writeProjectXMLToList()`	Write a project.xml file from StoX <= 2.7 from a list

Reference

All functions