Merge pull request #425 from StoXProject/StoXv4.1.0

Corrected error in HLNoAtLngt in ICESDatras().

Author: arnejohannesholmin

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RstoxData
-Version: 2.1.4-9001
-Date: 2025-03-21
+Version: 2.1.4-9002
+Date: 2025-03-26
 Title: Tools to Read and Manipulate Fisheries Data
 Authors@R: c(
   person(given = "Edvin", 

NEWS.md

@@ -1,3 +1,7 @@
+# RstoxData v2.1.4-9002  (2025-03-26)
+* Corrected error in ICESDatras() where HLNoAtLngt was not properly set (Sex set to NA after HLNoAtLngt was calculated).
+
+
 # RstoxData v2.1.4-9001  (2025-03-21)
 * Changed ICESDatras() to output missing Sex in the HL table, and where TotalNo and NoMeas are now sums over all sexes (a consequence of setting Sex to NA). The reason for this change is that in Norwegian biotic data catch categories (sub-samples) are not separated by sex, which results in SubWgt and CatCatchWgt being sums over sexes. In other words, the resolution in the Norwegian biotic data is not by sex, hence the change to Sex set to NA in the HL table. The CA table is left unchanged.
 

R/StoxExport.R

@@ -1226,21 +1226,32 @@ ICESDatrasOne <- function(
 	### 	mergedHL[lenInterval == interval, lngtClass := intVec[findInterval(length, intVec)]]
 	### }
 
+	
+	
 	# Count measured individual
 	mergedHL[!is.na(length), lsCountTot := 1]
 
-	# Aggregate hlNoAtLngth and lsCountTot
-	finalHL <- mergedHL[, .(N, lsCountTot = sum(lsCountTot)), by = c(
-		groupHL,  
-		"lngtClass", "Quarter", "Country", "Ship", "Gear", "SweepLngt", "GearEx", "DoorType", "HaulNo", "SpecVal", "catCatchWgt", "sampleFac", "subWeight", "lngtCode", "stationtype", "lengthmeasurement"
-		)
-	]
 
 	# To fix the problem that the procedure at the IMR is to not split sex into different subsamples, we set the sex to NA here, so that aggregation to produce noMeas and totalNo sum over sexes. The reason for this is that catCatchWgt and subWeight are in practice summed over sexes, and we do not want to do estimation to split these by sex.
+	finalHL <- mergedHL
 	finalHL[, sex := NA]
 
+	# Aggregate hlNoAtLngth and lsCountTot
+	# We ignore the defined aggregation variable devstage, as this is always NA in norwegian data (hard coded below):
+	finalHL <- finalHL[, lsCountTot := sum(lsCountTot), by = c(groupHL, "lngtClass")]
+	finalHL <- unique(finalHL, by = c(groupHL, "lngtClass"))
+	
+	#finalHL <- finalHL[, .(N, lsCountTot = sum(lsCountTot)), by = c(
+	#	groupHL,  
+	#	"lngtClass", "Quarter", "Country", "Ship", "Gear", "SweepLngt", "GearEx", "DoorType", "HaulNo", "SpecVal", "catCatchWgt", "sampleFac", "subWeight", "lngtCode", "stationtype", "lengthmeasurement"
+	#	)
+	#]
+	
+	# To fix the problem that the procedure at the IMR is to not split sex into different subsamples, we set the sex to NA here, so that aggregation to produce noMeas and totalNo sum over sexes. The reason for this is that catCatchWgt and subWeight are in practice summed over sexes, and we do not want to do estimation to split these by sex.
+	#finalHL[, sex := NA]
+	
 
-	finalHL <- finalHL[!duplicated(finalHL)]
+	#finalHL <- finalHL[!duplicated(finalHL)]
 	finalHL[,`:=`(noMeas = sum(lsCountTot)), by = groupHL]
 	finalHL[,`:=`(totalNo = noMeas * sampleFac, subFactor = sampleFac)]