Merge pull request #345 from StoXProject/datsusc

Datsusc
StoXProject · Nov 23, 2023 · 5d129b8 · 5d129b8
2 parents 0ae9405 + bf22c7a
commit 5d129b8
Show file tree

Hide file tree

Showing 23 changed files with 679 additions and 37 deletions.
diff --git a/.github/workflows/check-full.yaml b/.github/workflows/check-full.yaml
@@ -291,4 +291,4 @@ jobs:
           tag: ${{ env.FINAL_TAG }}
           name: ${{ env.FINAL_TAG }}
           artifacts: ${{ env.PKG_REPO }}/${{ env.PKG_FREL }}
-          token: ${{ secrets.GITHUB_TOKEN }}
+          token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: RstoxData
 Version: 1.10.2-9003
-Date: 2023-11-22
+Date: 2023-11-23
 Title: Tools to Read and Manipulate Fisheries Data
 Authors@R: c(
   person(given = "Edvin", 

diff --git a/NAMESPACE b/NAMESPACE
@@ -11,6 +11,7 @@ export(CopyBiotic)
 export(CopyICESAcoustic)
 export(CopyICESBiotic)
 export(CopyICESDatras)
+export(CopyICESDatsusc)
 export(CopyLanding)
 export(CopyStoxAcoustic)
 export(CopyStoxBiotic)
@@ -21,13 +22,15 @@ export(FilterBiotic)
 export(FilterICESAcoustic)
 export(FilterICESBiotic)
 export(FilterICESDatras)
+export(FilterICESDatsusc)
 export(FilterLanding)
 export(FilterStoxAcoustic)
 export(FilterStoxBiotic)
 export(FilterStoxLanding)
 export(ICESAcoustic)
 export(ICESBiotic)
 export(ICESDatras)
+export(ICESDatsusc)
 export(MergeAcoustic)
 export(MergeStoxAcoustic)
 export(MergeStoxBiotic)
@@ -45,6 +48,7 @@ export(TranslateBiotic)
 export(TranslateICESAcoustic)
 export(TranslateICESBiotic)
 export(TranslateICESDatras)
+export(TranslateICESDatsusc)
 export(TranslateLanding)
 export(TranslateStoxAcoustic)
 export(TranslateStoxBiotic)

diff --git a/R/Copy.R b/R/Copy.R
@@ -153,6 +153,39 @@ CopyICESDatras <- function(
 	return(ICESDatrasDataCopy)
 }
 
+##################################################
+#' Copy a variable of ICESDatrasData
+#' 
+#' This function copies a variable to another (possibly existing) variable of \code{\link{ICESDatrasData}} .
+#' 
+#' @inheritParams ModelData
+#' @inheritParams copy_arguments
+#' 
+#' @return
+#' A \code{\link{ICESDatrasData}} object.
+#' 
+#' @export
+#' 
+CopyICESDatsusc <- function(
+    ICESDatsuscData, 
+    FromVariable = character(), 
+    ToVariable = character(), 
+    Overwrite = FALSE, 
+    PreserveClass = TRUE
+) {
+  # Make a copy, as we are copying by reference:
+  ICESDatsuscDataCopy <- data.table::copy(ICESDatsuscData)
+
+  copyData(
+    data = ICESDatsuscDataCopy, 
+    fromVariable = FromVariable,
+    toVariable = ToVariable,
+    overwrite = Overwrite,
+    preserveClass = PreserveClass
+  )
+
+  return(ICESDatsuscDataCopy)
+}
 
 ##################################################
 #' Copy a variable of AcousticData

diff --git a/R/DefineAndUpdateVariables.R b/R/DefineAndUpdateVariables.R
@@ -945,6 +945,47 @@ TranslateICESDatras <- function(
 	return(ICESDatrasDataCopy)
 }
 
+##################################################
+#' Translate ICESDatsuscData
+#' 
+#' This function translates one or more columns of \code{\link{ICESDatsuscData}} to new values given by the input \code{Translation}.
+#' 
+#' @inheritParams DefineTranslation
+#' @inheritParams ModelData
+#' @inheritParams ProcessData
+#' @inheritParams TranslateStoxBiotic
+#' 
+#' @return
+#' A \code{\link{ICESDatsuscData}} object.
+#' 
+#' @export
+#' 
+TranslateICESDatsusc <- function(
+    ICESDatsuscData, 
+    TranslationDefinition = c("FunctionParameter", "FunctionInput"), 
+    VariableName = character(),
+    Conditional = FALSE, # If TRUE, adds a column to the parameter format translationTable.
+    ConditionalVariableNames = character(),
+    TranslationTable = data.table::data.table(), 
+    Translation,  
+    PreserveClass = TRUE
+) {
+  # Make a copy, as we are translating by reference:
+  ICESDatsuscDataCopy <- data.table::copy(ICESDatsuscData)
+
+  translateVariables(
+    data = ICESDatsuscDataCopy, 
+    TranslationDefinition = TranslationDefinition, 
+    TranslationTable = TranslationTable, 
+    VariableName = VariableName,
+    Conditional = Conditional,
+    ConditionalVariableNames = ConditionalVariableNames,
+    Translation = Translation,  
+    PreserveClass = PreserveClass
+  )
+
+  return(ICESDatsuscDataCopy)
+}
 
 
 

diff --git a/R/Filter.R b/R/Filter.R
@@ -696,3 +696,28 @@ FilterICESDatras <- function(ICESDatrasData, FilterExpression = list()) {
 	return(ICESDatrasData)
 }
 
+#' Filter ICESDatsusc data
+#'
+#' Filters \code{\link{ICESDatsuscData}}.
+#' 
+#' @param ICESDatsuscData  Input \code{\link{ICESDatsuscData}} data.
+#' @param FilterExpression Filter expression in list of strings. The name of the list and structures should be identical to the names of the input data list.
+#'
+#' @return An object of filtered data in the same format as the input data.
+#'
+#' @export
+#' 
+FilterICESDatsusc <- function(ICESDatsuscData, FilterExpression = list()) {
+  # For filtering directly on the input data, we need to split the list filter expression to one level for the file and one for the table:
+  #FilterExpression <- expandFilterExpressionList(FilterExpression)
+
+  ICESDatsuscData <- filterData(
+    ICESDatsuscData, 
+    filterExpression = FilterExpression, 
+    propagateDownwards = TRUE, 
+    propagateUpwards = FALSE
+  )
+
+  return(ICESDatsuscData)
+}
+
diff --git a/R/RstoxData-package.R b/R/RstoxData-package.R
@@ -14,35 +14,39 @@ utils::globalVariables(c(
 	 "..colList", "..columns", "..groupingVariables", "..keep", "..parameterNames",
 	 "..relevantColumns", "..replacement", "..sourceColumns", "..targetAndSourceVariables",
 	 "..toKeep", "..valueVariablesInTranslation", "..varToExtract", "..variableKeys",
-	 "..variablesInTable", "..x", "AcousticCategory", "Addition", "BeamKey", "CANoAtLngt",
-	 "Channel", "ChannelDepthLower", "ChannelDepthUpper", "ChannelReferenceKey",
-	 "ChannelReferenceType", "Constant", "Country", "Cruise", "CruiseKey", "DateTime", "DoorType",
-	 "EDSU", "EchoType", "EffectiveTowDistance", "FishID", "Frequency", "Gear", "GearEx",
-	 "HLNoAtLngt", "HaulNo", "ID", "LngtClass", "LngtCode", "LocalID", "LogKey", "N", "NewValue",
-	 "NumberAtLength", "NumberOfIndividualsToGenerate", "NumberOfSampledIndividuals", "Quarter",
-	 "ReplaceBy", "ResolutionCode", "SaCategory", "Scaling", "Ship", "SpecVal",
-	 "SpeciesCategoryNumber", "SpeciesCategoryWeight", "SpeciesCode", "StatRec", "SubsampleWeight",
-	 "SubsampledNumber", "Survey", "SweepLngt", "Time", "TransducerOrientation", "Value",
-	 "VariableName", "WeightMeasurement", "acocat", "age", "agingstructure", "aphia",
-	 "bottomdepthstart", "bottomdepthstop", "catCatchWgt", "catchcount", "catchpartnumber",
+	 "..variablesInTable", "..x", "AcousticCategory", "Addition", "AphiaIDPredator", "AphiaIDPrey",
+	 "BeamKey", "CANoAtLngt", "Channel", "ChannelDepthLower", "ChannelDepthUpper",
+	 "ChannelReferenceKey", "ChannelReferenceType", "Constant", "Count", "Country", "Cruise",
+	 "CruiseKey", "DateTime", "Day", "DigestionStage", "DoorType", "EDSU", "EchoType",
+	 "EffectiveTowDistance", "FishID", "Frequency", "Gear", "GearEx", "GravMethod", "HLNoAtLngt",
+	 "HaulNo", "ICESDatsucsData", "ID", "IdentMet", "LngtClass", "LngtCode", "LocalID", "LogKey",
+	 "Month", "N", "NewValue", "Number", "NumberAtLength", "NumberOfIndividualsToGenerate",
+	 "NumberOfSampledIndividuals", "PreySequence", "Quarter", "ReplaceBy", "ResolutionCode",
+	 "SaCategory", "Scaling", "Ship", "SpecVal", "SpeciesCategoryNumber", "SpeciesCategoryWeight",
+	 "SpeciesCode", "StatRec", "StationNumber", "StomachFullness", "SubFactor", "SubsampleWeight",
+	 "SubsampledNumber", "Survey", "SweepLngt", "Time", "TotalCount", "TransducerOrientation",
+	 "Value", "VariableName", "WeightMeasurement", "Year", "acocat", "age", "agingstructure",
+	 "aphia", "bottomdepthstart", "bottomdepthstop", "catCatchWgt", "catchcount", "catchpartnumber",
 	 "catchproducttype", "catchweight", "ch", "cruise", "currentReportingUnit", "direction",
 	 "distance", "fishingdepthcount", "fishingdepthmax", "fishingdepthmin", "freq", "gear",
-	 "gearflow", "inapplicableFormats", "individualweight", "integrator_dist", "iskey", "lat_start",
-	 "lat_stop", "latitudeend", "latitudestart", "lengthCode", "lengthmeasurement",
-	 "lengthresolution", "lengthsamplecount", "lengthsampleweight", "level", "liverweight",
-	 "lngtClass", "lngtCode", "log_start", "logstart", "lon_start", "lon_stop", "longitudeend",
-	 "longitudestart", "lsCountTot", "maturity", "maxFishID", "max_bot_depth", "meanW",
-	 "missionstartdate", "missionstopdate", "nInd", "nation", "newClass", "newLngtCode",
-	 "newLngtCodeNumeric", "newReportingUnit", "noMeas", "parasite", "pel_ch_thickness", "platform",
-	 "platformname", "preferredagereading", "readability", "reportingUnit", "res", "sa",
-	 "sampleFac", "serialnumber", "sex", "shortname", "specialstage", "specimenid", "start_time",
-	 "startyear", "station", "stationstartdate", "stationstarttime", "stationstopdate",
-	 "stationstoptime", "stomach", "stoxBioticObject", "subFactor", "subWeight", "suffixes",
-	 "sum_sa.x", "sum_sa.y", "sweeplength", "tagid", "tagtype", "target", "threshold",
-	 "tissuesample", "totalNo", "transceiver", "translationListOne", "trawldoorarea",
-	 "trawldoorspread", "trawldoortype", "trawldoorweight", "variableToTranslate",
-	 "verticaltrawlopening", "vesselspeed", "winddirection", "windspeed", "wingspread",
-	 "wiredensity", "wirediameter", "wirelength", "xsdObjects"))
+	 "gearflow", "i.replace_number", "inapplicableFormats", "individualweight", "integrator_dist",
+	 "interval", "iskey", "lat_start", "lat_stop", "latitudeend", "latitudestart", "lengthCode",
+	 "lengthintervalcount", "lengthintervalstart", "lengthmeasurement", "lengthresolution",
+	 "lengthsamplecount", "lengthsampleweight", "level", "liverweight", "lngtClass", "lngtCode",
+	 "log_start", "logstart", "lon_start", "lon_stop", "longitudeend", "longitudestart",
+	 "lsCountTot", "maturity", "maxFishID", "max_bot_depth", "meanW", "missionstartdate",
+	 "missionstopdate", "nInd", "nation", "newClass", "newLngtCode", "newLngtCodeNumeric",
+	 "newReportingUnit", "noMeas", "parasite", "pel_ch_thickness", "platform", "platformname",
+	 "preferredagereading", "preycategory", "preydigestion", "preyforeignobject", "preysampleid",
+	 "readability", "reportingUnit", "res", "sa", "sampleFac", "serialnumber", "sex", "shortname",
+	 "specialstage", "specimenid", "start_time", "startyear", "station", "stationstartdate",
+	 "stationstarttime", "stationstopdate", "stationstoptime", "stomach", "stomachfillfield",
+	 "stomachweight", "stoxBioticObject", "subFactor", "subWeight", "suffixes", "sum_sa.x",
+	 "sum_sa.y", "sweeplength", "tagid", "tagtype", "target", "threshold", "tissuesample",
+	 "totalNo", "totalweight", "transceiver", "translationListOne", "trawldoorarea",
+	 "trawldoorspread", "trawldoortype", "trawldoorweight", "uniqueN", "variableToTranslate",
+	 "verticaltrawlopening", "vesselspeed", "weightresolution", "winddirection", "windspeed",
+	 "wingspread", "wiredensity", "wirediameter", "wirelength", "xsdObjects"))
 
 .onLoad <- function(libname, pkgname) {
 	# Initiate the RstoxData environment: