Merge pull request #255 from StoXProject/develop

Develop

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RstoxData
-Version: 1.7.3
-Date: 2022-11-14
+Version: 1.7.4-9001
+Date: 2022-11-18
 Title: Tools to Read and Manipulate Fisheries Data
 Authors@R: c(
   person(given = "Edvin", 

NAMESPACE

@@ -57,6 +57,7 @@ export(getRstoxDataDefinitions)
 export(getStoxKeys)
 export(getUnit)
 export(getUnitOptions)
+export(hasUnit)
 export(is.LandingData)
 export(is.StoxLandingData)
 export(lapplyOnCores)

NEWS.md

@@ -1,5 +1,14 @@
+# RstoxData v1.7.3-9002  (2022-11-17)
+* Fixed typo in warning for more sa in B than in P.
+* Added a unique fo the Log table in StoxAcoustic for ICESAcoutsic.
+* Added units for area number density, and one for megaton.
+* Added the exported hasUnit().
+
+
+# RstoxData v1.7.3-9001  (2022-11-15)
+* Fixed bug in ReadAcoustic when an ICESAcoustic xml files contains more than one instrument.
+
 # RstoxData v1.7.2  (2022-11-13)
-* Added warning when an ICESAcoustic xml files contains more than one instrument, in which case the xml file does not contain enough information for StoX to link the Sample and Data tables.
 * Fixed bug with R < 4.2, where a filter process with unspecified FilterExpression retuns error "zero-length inputs cannot be mixed with those of non-zero length". The error is returned both when opening the FilterExpression and when running the process.
 
 # RstoxData v1.7.1-9002  (2022-10-31)

R/StoxAcoustic.R

@@ -261,7 +261,7 @@ StoxAcousticOne <- function(data_list) {
 			sum_sa_merged_onlyError <- sum_sa_merged_onlyError[, do.call(paste, c(.SD, list(sep = " - ")))]
 
 			if(NROW(sum_sa_merged_onlyError)) {
-				warning("StoX: There are data of the file ", data_list$metadata$file, " that contain more sa in ch_type \"B\" than \"P\". This coculd be an indication of loss of data from raw files + work files (scrutinization) to the NMDEchosounder file. The problem occurs for the following cruise, log-distance, frequency and sum of sa for \"P\" and \"B\" (CruiseKey - LogKey - BeamKey - Sum_of_NASC_for_P - Sum_of_NASC_for_P):", printErrorIDs(sum_sa_merged_onlyError))
+				warning("StoX: There are data of the file ", data_list$metadata$file, " that contain more sa in ch_type \"B\" than \"P\". This coculd be an indication of loss of data from raw files + work files (scrutinization) to the NMDEchosounder file. The problem occurs for the following cruise, log-distance, frequency and sum of sa for \"P\" and \"B\" (CruiseKey - LogKey - BeamKey - Sum_of_NASC_for_P - Sum_of_NASC_for_B):", printErrorIDs(sum_sa_merged_onlyError))
 			}
 		}
 
@@ -304,7 +304,6 @@ StoxAcousticOne <- function(data_list) {
 
 
 	else{
-
 		#################################################################
 		# Description: protocol to convert ICESacoustic to StoxAcoustic #
 		#################################################################
@@ -319,22 +318,16 @@ StoxAcousticOne <- function(data_list) {
 		#         Fiks to correct time format, and add to key           #
 		#################################################################
 		#data_list$Log[, LogKey:= paste0(gsub(' ','T',Time),'.000Z')]
+		data_list$Log <- unique(data_list$Log)
+
 		data_list$Log[, LogKey := getLogKey_ICESAcoustic(Time)]
 
 		data_list$Log[, EDSU:= paste(LocalID,LogKey,sep='/')]
 
-		#browser()
 
 		#################################################################
 		#                   MAKE other general level                    #
 		#################################################################
-		# ICESACoustic does not seem to support multiple frequencies in the XML format, as Instrument is present in the Sample table but not in the Data table:
-		uniqueInstruments <- data_list$Sample[, unique(Instrument)]
-		if(length(uniqueInstruments) > 1) {
-			stop("The ICESAcoutsic XML file ", data_list$metadata$file, " contain multiple Instruments. However StocAcoustic can currently not convert data from ICESAcoutsic XML format as the Instrument tag is presesnt in the Sample but not the Data table.")
-		}
-
-
 		tmp <- merge(data_list$Sample,data_list$NASC)
 		tmp <- merge(tmp,data_list$Log[,c('Distance','Time','LogKey','Origin')],by='Distance')
 		names(tmp)[names(tmp)=="Instrument"]='ID'

R/readXmlFile.R

@@ -155,17 +155,22 @@ icesAcousticPreprocess <- function(xsdObject) {
 
 	newAC$prefixLens[allDatawithPrefix] <- 1
 	newAC$prefixLens["Log"] <- 2
-	newAC$prefixLens["Sample"] <- 3
-	newAC$prefixLens["Data"] <- 4
+	newAC$prefixLens["Sample"] <- 4
+	newAC$prefixLens["Data"] <- 5
 
 	newAC$tableHeaders$Log <- c("LocalID", newAC$tableHeaders$Log)
 	newAC$tableTypes$Log <- c("xsd:string", newAC$tableTypes$Log)
 
-	newAC$tableHeaders$Sample <- c("LocalID", "Distance", newAC$tableHeaders$Sample)
-	newAC$tableTypes$Sample <- c("xsd:string", "xsd:float", newAC$tableTypes$Sample)
+	# We need here to add Instrument as the first header, since it must serve as a key:
+	newAC$tableHeaders$Sample <- c("LocalID", "Distance", "Instrument", newAC$tableHeaders$Sample)
+	newAC$tableTypes$Sample <- c("xsd:string", "xsd:float", "xsd:string", newAC$tableTypes$Sample)
+	# Remove the duplicated Instrument:
+	atDup <- duplicated(newAC$tableHeaders$Sample)
+	newAC$tableHeaders$Sample <- newAC$tableHeaders$Sample[!atDup]
+	newAC$tableTypes$Sample <- newAC$tableTypes$Sample[!atDup]
 
-	newAC$tableHeaders$Data <- c("LocalID", "Distance", "ChannelDepthUpper", newAC$tableHeaders$Data)
-	newAC$tableTypes$Data <- c("xsd:string", "xsd:float",  "xsd:float", newAC$tableTypes$Data)
+	newAC$tableHeaders$Data <- c("LocalID", "Distance", "Instrument", "ChannelDepthUpper", newAC$tableHeaders$Data)
+	newAC$tableTypes$Data <- c("xsd:string", "xsd:float", "xsd:string", "xsd:float", newAC$tableTypes$Data)
 
 
 	# Modify cruise structure to get LocalID as prefix (the types order are the same, as they are all type of string)

R/units.R

@@ -165,6 +165,22 @@ getUnit <- function(value, property=c("id", "shortname", "symbol", "name"), unit
 
 }
 
+#' Does the input have unit?
+#' @description 
+#'  Get unit id, shortname, symbol or name of a value in accordance with StoX convention.
+#' @inheritParams getUnit
+#' @return TRUE if the \code{value} has unit, FALSE if not.
+#' @examples 
+#'  dt <- data.table::data.table(weight=c(1000,1200))
+#'  dt$weight <- setUnit(dt$weight, "mass-g")
+#'  print(hasUnit(dt$weight))
+#'  print(hasUnit(1))
+#' @export
+hasUnit <- function(value, property=c("id", "shortname", "symbol", "name"), unitTable=RstoxData::StoxUnits){
+	unit <- getUnit(value, property=property, unitTable=unitTable)
+	!is.na(unit)
+}
+
 #' Get available units
 #' @description 
 #'  Get the unit shortnames, symbols or names that are available for a given quantity.

inst/prepResources/prepUnits.R → data-raw/prepUnits.R

@@ -10,6 +10,10 @@
 # Typically, the user "sees" shortname, symbol and name.
 # 
 
+
+setwd(file.path(getwd(), "RstoxData"))
+setwd(file.path(getwd(), "data-raw"))
+
 StoxUnits <- data.table::data.table(id=character(),
                                     quantity=character(),
                                     symbol=character(),
@@ -21,16 +25,25 @@ StoxUnits <- rbind(StoxUnits, list("mass-g", "mass", "g", "g", "gram", 1e-3))
 StoxUnits <- rbind(StoxUnits, list("mass-kg", "mass", "kg", "kg", "kilogram", 1))
 StoxUnits <- rbind(StoxUnits, list("mass-ton", "mass", "t", "ton", "metric ton", 1e3))
 StoxUnits <- rbind(StoxUnits, list("mass-kt", "mass", "kt", "kiloton", "kiloton", 1e6))
+StoxUnits <- rbind(StoxUnits, list("mass-Mt", "mass", "Mt", "megaton", "megaton", 1e9))
+
 StoxUnits <- rbind(StoxUnits, list("length-mm", "length", "mm", "mm", "millimeter", 1e-3))
 StoxUnits <- rbind(StoxUnits, list("length-cm", "length", "cm","cm", "centimeter", 1e-2))
 StoxUnits <- rbind(StoxUnits, list("length-m", "length", "m", "m", "meter", 1))
 StoxUnits <- rbind(StoxUnits, list("length-km", "length", "km", "km", "kilometer", 1e3))
 StoxUnits <- rbind(StoxUnits, list("length-nmi", "length", "M", "nmi", "nautical mile", 1852)) #M is hydrographic standard
+
 StoxUnits <- rbind(StoxUnits, list("cardinality-N", "cardinality", "N", "individuals", "individuals", 1))
 StoxUnits <- rbind(StoxUnits, list("cardinality-kN", "cardinality", "kN", "10^3 individuals", "thousand individuals", 1e3))
 StoxUnits <- rbind(StoxUnits, list("cardinality-MN", "cardinality", "MN", "10^6 individuals", "million individuals", 1e6))
+
+StoxUnits <- rbind(StoxUnits, list("area_number_density-N/nmi^2", "area_number_density", "N/nmi^2", "individuals/nmi^2", "individuals per sqare nautical mile", 1))
+StoxUnits <- rbind(StoxUnits, list("area_number_density-kN/nmi^2", "area_number_density", "kN/nmi^2", "10^3 individuals/nmi^2", "thousand individuals per sqare nautical mile", 1e3))
+StoxUnits <- rbind(StoxUnits, list("area_number_density-MN/nmi^2", "area_number_density", "MN/nmi^2", "10^6 individuals/nmi^2", "million individuals per sqare nautical mile", 1e6))
+
 StoxUnits <- rbind(StoxUnits, list("fraction-decimal", "fraction", "0.", "fraction", "decimal", 1))
 StoxUnits <- rbind(StoxUnits, list("fraction-percent", "fraction", "%", "%", "percent", 1e-2))
+
 # treat age separate from time, as it is not a fixed ratio to actual time units
 StoxUnits <- rbind(StoxUnits, list("age-year", "age", "y", "year", "year", 1))
 StoxUnits <- rbind(StoxUnits, list("time-s", "time", "s", "second", "second", 1))