Merge pull request #423 from StoXProject/develop

Develop

Author: arnejohannesholmin

Diff for: DESCRIPTION

@@ -1,5 +1,5 @@
 Package: RstoxData
-Version: 2.1.3
+Version: 2.1.4-9001
 Date: 2025-03-21
 Title: Tools to Read and Manipulate Fisheries Data
 Authors@R: c(

Diff for: NEWS.md

@@ -1,4 +1,8 @@
-# RstoxData v2.1.3  (2025-03-21)
+# 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.
+
+
+RstoxData v2.1.3  (2025-03-21)
 * Fixed error in ReadBiotic() and ReadAcoustic() where autodetectXml() returned \"Memory allocation failed\" on Windows due to imcomplete XML returned by readCharZip() not beeing accepted by xml2 v1.3.7 and v1.3.8.
 * Adding area_number_density-GN/nmi^2 unit.
 * Changed to point to getOption("repos") instead of "https://cloud.r-project.org/" in install.packages() in README.md, so that we do not override the users repo settings.

Diff for: R/StoxExport.R

@@ -1236,6 +1236,10 @@ ICESDatrasOne <- function(
 		)
 	]
 
+	# 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[,`:=`(noMeas = sum(lsCountTot)), by = groupHL]
 	finalHL[,`:=`(totalNo = noMeas * sampleFac, subFactor = sampleFac)]

Diff for: R/data.R

@@ -471,7 +471,7 @@ NULL
 #' Biotic data stored in the ICESDatras (CSV) format.
 #' 
 #' @details
-#' This StoX data type is produced by \code{\link{ICESDatras}}, and contains one list per input biotic file read to produec the input to \code{\link{ICESDatras}}, each holding the tables HH, HL and CA, in that hierarchical order.
+#' This StoX data type is produced by \code{\link{ICESDatras}}, and contains one list per input biotic file read to produec the input to \code{\link{ICESDatras}}, each holding the tables HH, HL and CA, in that hierarchical order. See the \href{https://www.ices.dk/data/Documents/DATRAS/DATRAS_Field_descriptions_and_example_file_March2024.xlsx}{relevant DATRAS format description updated March 2024}.
 #' 
 #' @seealso \code{\link{DataTypes}} for a list of all StoX data types produced by \code{\link{RstoxData}}
 #'