Man pages for StoXProject/RstoxBase
Base StoX 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 |
| aggregateBaselineDataOneTable | Function to aggregate baseline data |
| aggregateBaselineDataOneTableSingleFunction | Function to aggregate baseline data |
| allargs | Get all arguments from inside a function |
| allEqual | Test whether all values are equal. |
| AppendNASC | Append to NASCData |
| AssignmentLengthDistribution | Assignment length distribution per acoustic PSU |
| AssignmentLengthDistributionData | Assignment length distribution data |
| backwardCompatibility_RstoxBase | Backward compabitibility actions: |
| 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 |
| combined.color | Combined rainbow and desaturation color scale |
| cv | The coefficient of variation, i.e., the standard deviation... |
| 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 |
| factorNAfirst | Convert to factor and put NAs first |
| filterTable | Filter a table |
| formatOutput | Function to format the output of a function returning StoX... |
| formatProcessData | Format process data |
| fractionOfOccurrence | The fraction of occurrence function |
| fractionOfSum | The fraction of occurrence function |
| 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) |
| general_arguments | General parameters of RstoxBase |
| general_arguments2.7 | General parameters of treating project.xml file from StoX <=... |
| 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... |
| getProjectXMLFilePath | Get the path to the project.xml file from StoX <= 2.7. |
| getReportFunctions | Function returning the report functions defined for reporting... |
| getReportFunctionVariableName | Get the name of the target variable after aggregating. |
| getRstoxBaseDefinitions | Get RstoxBase definitions |
| getSeedVector | Generate a seed vector consistently |
| getStratumNames | Extract or add stratum names from a SpatialPolygonsDataFrame |
| hasBaseUnit | Does the variable of the StoX dataType have a base unit? |
| 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... |
| 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 |
| modifyParameter_ProjectXMLList | Modify a parameter of a process of a list representation of a... |
| modifyProj4String | Define a proj4 string |
| NASC | NASC |
| NASCData | Nautical area scattering coefficient (NASC) data |
| NASCToStoxAcoustic | Convert NASCData to StoxAcousticData |
| number | Number of TRUE |
| PlotAcousticTrawlSurvey | Plot NASCData |
| PlotAcousticTrawlSurveyData | Plot Acoustic-Trawl Survey data |
| PreySpeciesCategoryCatch | Table of total catch weight and number per Haul and... |
| PreySpeciesCategoryCatchData | Total prey catch per PreySpeciesCategory and Individual |
| ProcessData | Process data used by RstoxBase |
| processPropertyFormats | Define the process property formats: |
| PSU | Acoustic and biotic primary sampling units |
| Quantity | Calculate abundance in the strata |
| QuantityData | Quantity data |
| readAcousticPSUFrom2.7 | Read a the AcousticPSU from a project.xml file from StoX <=... |
| readBioticAssignmentFrom2.7 | Read a the BioticAssignment from a project.xml file from StoX... |
| readBioticPSUFrom2.7 | Read a the AcousticPSU from a project.xml file from StoX <=... |
| readProjectXMLToList | Read a project.xml file from StoX <= 2.7 |
| readStratumPolygonFrom2.7 | Read a the StratumPolygon from a project.xml file from StoX... |
| Regression | Regression |
| RegroupLengthDistribution | Regroup length distribution to common intervals |
| RelativeLengthDistribution | Relative length distribution |
| renameSSULabelInPSUProcessData | Rename SSU to either EDSU or Station |
| replaceNAByReference | Replace all NAs in a data.table by reference |
| 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 | Base StoX Functions |
| 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 |
| SpeciesCategoryCatch | Table of total catch weight and number per Haul and... |
| SpeciesCategoryCatchData | Total catch per SpeciesCategory and Haul |
| SplitMeanNASC | Split MeanNASCData to NASCData (deprecated) |
| SplitNASC | Split NASCData |
| Station | Horizontal input resolution for swept-area models |
| StoxDataStartMiddleStopDateTime | Generate Start, Middle and Stop DateTime variables |
| stoxFunctionAttributes | A list of the attributes of the exported StoX functions: The... |
| StoX_multipolygon_WKT | StoX multipolygon WKT |
| 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 |
| summaryStox | The summary function introduced in StoX <= 2.7. |
| 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 |
| toJSON_Rstox | Convert to JSON |
| writeProjectXMLToList | Write a project.xml file from StoX <= 2.7 from a list |
| WriteStratumPolygon | Write StratumPolygon |
| WriteStratumPolygonData | Write StratumPolygon data |
