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Version 1.9.0-9002, see NEWS.md.
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‎DESCRIPTION

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Package: RstoxData
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Version: 1.9.0-9001
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Date: 2023-02-24
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Version: 1.9.0-9002
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Date: 2023-03-06
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Title: Tools to Read and Manipulate Fisheries Data
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Authors@R: c(
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person(given = "Edvin",

‎NEWS.md

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# RstoxData v1.9.0-90010 (2023-01-19 )
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# RstoxData v1.9.0-9002 (2023-03-06)
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* Updated documentation of StoxAcoustic and StoxBiotic with tables defining each variable.
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* Added unit specification of StoxAcoustic and StoxBiotic variables.
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* Removed error when filtering BioticData read from ICESBiotic and ICESAcoustic XML.
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* Fixed snprintf warnnings.
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# RstoxData v1.9.0-9001 (2023-01-19)
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* Corrected warning " There are more than one 'serialnumber' ..." to end with "More than one serialnumber for the following cruise/station (of the fishstation table of the BioticData):" instead of "Duplicated serialnumber for the following cruise/station (of the fishstation table of the BioticData):".
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* Corrected warning for more NASC in B than in P.
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* Corrected warninig for non-supported NMDEhcosounder format from >= 1.4 to >= 1.1.

‎R/Definitions.R

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@@ -67,6 +67,108 @@ initiateRstoxData <- function(){
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# )
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#)
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#### Data type units: ####
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dataTypeUnits <- list(
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# Quantity:
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StoxAcoustic = list(
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# Cruise level:
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CruiseKey = list(quantity = "NA", unit = "NA"),
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Cruise = list(quantity = "NA", unit = "NA"),
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Platform = list(quantity = "NA", unit = "NA"),
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# Log level:
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LogKey = list(quantity = "NA", unit = "NA"),
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Log = list(quantity = "NA", unit = "NA"),
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EDSU = list(quantity = "NA", unit = "NA"),
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DateTime = list(quantity = "datetime", unit = "ISO8601"),
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Longitude = list(quantity = "angle", unit = "degree east"),
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Latitude = list(quantity = "angle", unit = "degree north"),
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LogOrigin = list(quantity = "NA", unit = "NA"),
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Longitude2 = list(quantity = "angle", unit = "degree east"),
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Latitude2 = list(quantity = "angle", unit = "degree north"),
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LogOrigin2 = list(quantity = "NA", unit = "NA"),
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LogDistance = list(quantity = "length", unit = "nmi"),
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LogDuration = list(quantity = "time", unit = "s"),
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EffectiveLogDistance = list(quantity = "length", unit = "nmi"),
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BottomDepth = list(quantity = "length", unit = "m"),
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# Beam level:
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BeamKey = list(quantity = "NA", unit = "NA"),
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Beam = list(quantity = "NA", unit = "NA"),
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Frequency = list(quantity = "frequency", unit = "hertz"),
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# AcousticCategory level:
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AcousticCategoryKey = list(quantity = "NA", unit = "NA"),
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AcousticCategory = list(quantity = "NA", unit = "NA"),
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# ChannelReference level:
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ChannelReferenceKey = list(quantity = "NA", unit = "NA"),
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ChannelReferenceType = list(quantity = "NA", unit = "NA"),
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ChannelReferenceDepth = list(quantity = "length", unit = "m"),
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ChannelReferenceTilt = list(quantity = "angle", unit = "degree"),
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# NASC level:
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NASCKey = list(quantity = "NA", unit = "NA"),
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Channel = list(quantity = "NA", unit = "NA"),
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MaxChannelRange = list(quantity = "length", unit = "m"),
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MinChannelRange = list(quantity = "length", unit = "m"),
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NASC = list(quantity = "NASC", unit = "m^2/nmi^2")
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),
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StoxBiotic = list(
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# Cruise level:
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CruiseKey = list(quantity = "NA", unit = "NA"),
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Cruise = list(quantity = "NA", unit = "NA"),
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Platform = list(quantity = "NA", unit = "NA"),
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# Station level:
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StationKey = list(quantity = "NA", unit = "NA"),
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Station = list(quantity = "NA", unit = "NA"),
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CatchPlatform = list(quantity = "NA", unit = "NA"),
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DateTime = list(quantity = "datetime", unit = "ISO8601"),
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Longitude = list(quantity = "angle", unit = "degree east"),
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Latitude = list(quantity = "angle", unit = "degree north"),
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BottomDepth = list(quantity = "length", unit = "m"),
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# Haul level:
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HaulKey = list(quantity = "NA", unit = "NA"),
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Haul = list(quantity = "NA", unit = "NA"),
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Gear = list(quantity = "NA", unit = "NA"),
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TowDistance = list(quantity = "length", unit = "nmi"),
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EffectiveTowDistance = list(quantity = "length", unit = "nmi"),
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MinHaulDepth = list(quantity = "length", unit = "m"),
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MaxHaulDepth = list(quantity = "length", unit = "m"),
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VerticalNetOpening = list(quantity = "length", unit = "m"),
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HorizontalNetOpening = list(quantity = "lengthlength", unit = "m"),
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TrawlDoorSpread = list(quantity = "length", unit = "m"),
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# SpeciesCategory level:
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SpeciesCategoryKey = list(quantity = "NA", unit = "NA"),
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SpeciesCategory = list(quantity = "NA", unit = "NA"),
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# Sample level:
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SampleKey = list(quantity = "NA", unit = "NA"),
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Sample = list(quantity = "NA", unit = "NA"),
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CatchFractionWeight = list(quantity = "mass", unit = "kg"),
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CatchFractionNumber = list(quantity = "cardinality", unit = "individuals"),
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SampleWeight = list(quantity = "mass", unit = "kg"),
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SampleNumber = list(quantity = "cardinality", unit = "individuals"),
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# Individual level:
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IndividualKey = list(quantity = "NA", unit = "NA"),
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Individual = list(quantity = "NA", unit = "NA"),
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IndividualRoundWeight = list(quantity = "length", unit = "g"),
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IndividualTotalLength = list(quantity = "length", unit = "cm"),
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LengthResolution = list(quantity = "length", unit = "cm"),
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WeightMeasurement = list(quantity = "NA", unit = "NA"),
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IndividualAge = list(quantity = "age", unit = "year"),
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IndividualSex = list(quantity = "NA", unit = "NA")
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),
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SuperIndividualsData = list(
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IndividualTotalLength = list(quantity = "length", unit = "cm"),
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IndividualRoundWeight = list(quantity = "mass", unit = "g"),
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Abundance = list(quantity = "cardinality", unit = "individuals"),
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Biomass = list(quantity = "mass", unit = "g"),
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TowDistance = list(quantity = "length", unit = "nmi"),
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EffectiveTowDistance = list(quantity = "length", unit = "nmi"),
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CatchFractionWeight = list(quantity = "mass", unit = "kg"),
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CatchFractionNumber = list(quantity = "cardinality", unit = "individuals"),
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SampleWeight = list(quantity = "mass", unit = "kg"),
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SampleNumber = list(quantity = "cardinality", unit = "individuals"),
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IndividualAge = list(quantity = "age", unit = "year")
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)
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)
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targetAndSourceVariables <- list(
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target = "TargetVariable",
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source = "SourceVariable"

‎R/Filter.R

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if (!any(names(inputTables) %in% names(treeStruct)) & length(inputTables)>1){
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stop("Argument 'treeStruct' does not specify a hierarchy for 'inputTables'.")
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}
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if (length(treeStruct) >0 & !all(names(treeStruct) %in% names(inputTables))){
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stop("Argument 'treeStruct' does not specify a hierarchy for 'inputTables'.")
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}
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`%notin%` <- Negate(`%in%`)
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getTreestruct <- function(tables){
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#extract treeStruct for xsd
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if (!useXsd){
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levels <- names(tables)[names(tables) != "metadata"]
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levels <- setdiff(names(tables), "metadata")
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treeStruct <- as.list(tail(levels,-1))
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names(treeStruct) <- head(levels,-1)
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‎R/StoxAcoustic.R

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#'
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#' @return An object of StoX data type \code{\link{StoxAcousticData}}.
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#'
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#' @seealso The definition of the \code{\link[=StoxAcousticFormat]{StoxAcoustic format}} and \code{\link{generalSamplingHierarhcy}}.
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#'
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#' @export
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#'
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StoxAcoustic <- function(AcousticData){

‎R/StoxExport.R

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#' @param ICESAcousticData A \code{\link{ICESAcousticData}} object obtained from an ICES acoustic XML format file.
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#'
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#' @return List of string matrices in the ICES acoustic CSV format.
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#'
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#' @return An object of StoX data type \code{\link{WriteICESAcousticData}}.
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#'
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#' @export
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#'
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#'
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#' @param ICESBioticData A \code{\link{ICESBioticData}} object obtained from an ICES acoustic XML format file.
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#'
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#' @return List of string matrices in the ICES acoustic CSV format.
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#' @return #' @return An object of StoX data type \code{\link{WriteICESBioticData}}.
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#'
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#' @export
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WriteICESBiotic <- function(ICESBioticData){
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#'
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#' @inheritParams ModelData
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#'
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#' @return List of string matrices in the ICES Datras CSV format.
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#' @return An object of StoX data type \code{\link{WriteICESDatrasData}}.
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#'
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#' @export
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WriteICESDatras <- function(ICESDatrasData){

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