Merge pull request #432 from StoXProject/develop

Develop

Author: arnejohannesholmin

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: RstoxData
-Version: 2.1.4-9003
+Version: 2.1.4-9004
 Date: 2025-03-27
 Title: Tools to Read and Manipulate Fisheries Data
 Authors@R: c(

NEWS.md

@@ -1,3 +1,7 @@
+# RstoxData v2.1.4-9004  (2025-03-27)
+* Updated documentation on WriteICESDatrasData and WriteICESDatsucsData.
+
+
 # RstoxData v2.1.4-9003  (2025-03-27)
 * Corrected error in ICESDatras() where finalHL was not data.table copied from mergedHL, causing Sex to be NA in the CA table.
 

R/StoxExport.R

@@ -1953,10 +1953,7 @@ WriteICESDatrasOne <- function(ICESDatrasDataOne, na = "-9"){
 		ICESDatrasCSVDataOne <- lapply(ICESDatrasCSVDataOne, function(x) {x[is.na(x)] <- na; x})
 	}
 
-	#ICESDatrasCSVDataOne <- expandWidth(ICESDatrasCSVDataOne, na = na)
-	
-	# Stack all matrices:
-	#ICESDatrasCSVDataOne <- do.call(rbind, ICESDatrasCSVDataOne)
+	# IMPORTANT NOTE: The ICES DATRAS format assumes that the three tables HH, HL and CA are stacked in a comma separated file but without padding the tables to equal number of columns as is done for ICESAcoustic and ICESBiotic. For this reason we need to paste the data to a chatacter vector and write as lines. RstoxFramework detects that the output as a vector of characters and uses writeLines() to produce the file.
 
 	# Convert each line of each table to comma separated:
 	ICESDatrasCSVDataOne <- lapply(ICESDatrasCSVDataOne, apply, 1, paste, collapse = ",")
@@ -2222,6 +2219,10 @@ WriteICESDatsuscOne <- function(ICESDatsuscData, na = "-9"){
 	if(length(na)) {
 		ICESDatsuscCSVDataOne <- lapply(ICESDatsuscCSVDataOne, function(x) {x[is.na(x)] <- na; x})
 	}
+	
+	# IMPORTANT NOTE: The ICES DATRAS format assumes that the three tables HH, HL and CA are stacked in a comma separated file but without padding the tables to equal number of columns as is done for ICESAcoustic and ICESBiotic. For this reason we need to paste the data to a chatacter vector and write as lines. RstoxFramework detects that the output as a vector of characters and uses writeLines() to produce the file.
+	
+	
 	# Convert each line of each table to comma separated:
 	ICESDatsuscCSVDataOne <- lapply(ICESDatsuscCSVDataOne, apply, 1, paste, collapse = ",")
 	# Join to one vector, to be written to one file:

R/data.R

@@ -503,7 +503,7 @@ NULL
 #' The output of this function is suited for submission to \url{https://acoustic.ices.dk/}.
 #' 
 #' @details
-#' The ICESAcoustic CSV format is one string matrix containing all tables of \code{\link{ICESAcousticData}}, where column names are included as header rows.
+#' The ICESAcoustic CSV format is one string matrix containing all tables of \code{\link{ICESAcousticData}}, where column names are included as header rows. RstoxData appends columns with missing values in order to produce this matrix, and this is reflected in the output file written by RstoxFramework.
 #' 
 #' @seealso \code{\link{DataTypes}} for a list of all StoX data types produced by \code{\link{RstoxData}}
 #' 
@@ -518,7 +518,7 @@ NULL
 #' The output of this function is suited for submission to \url{https://acoustic.ices.dk/}.
 #' 
 #' @details
-#' The ICESBiotic CSV format is one string matrix containing all tables of \code{\link{ICESBioticData}}, where column names are included as header rows.
+#' The ICESBiotic CSV format is one string matrix containing all tables of \code{\link{ICESBioticData}}, where column names are included as header rows. RstoxData appends columns with missing values in order to produce this matrix, and this is reflected in the output file written by RstoxFramework.
 #' 
 #' @seealso \code{\link{DataTypes}} for a list of all StoX data types produced by \code{\link{RstoxData}}
 #' 
@@ -533,7 +533,7 @@ NULL
 #' The output of this function is suited for submission to \url{https://www.ices.dk/data/data-portals/Pages/DATRAS.aspx}.
 #' 
 #' @details
-#' The ICESDatras CSV format is one string matrix containing all tables of \code{\link{ICESDatrasData}}, where column names are included as header rows.
+#' The ICESDatras CSV format is a stack of comma separated tables containing all tables of \code{\link{ICESDatrasData}}, where column names are included as header rows. The file format does not contain the same number of elements in all rows, as the different tables are not padded with columns to produce a regular table. For this reason the output of \code{\link{WriteICESDatras}} is a character vector of comma separated strings representing the rows of the \code{\link{ICESDatrasData}}. The resulting output file written by RstoxFramework can for this reason not be read easily by e.g. \code{\link[data.table]{fread}}.
 #' 
 #' @seealso \code{\link{DataTypes}} for a list of all StoX data types produced by \code{\link{RstoxData}}
 #' 
@@ -549,7 +549,7 @@ NULL
 #' The output of this function is suited for submission to \url{https://www.ices.dk/data/data-portals/Pages/Stomach-content.aspx}.
 #' 
 #' @details
-#' The ICESDatras CSV format is one string matrix containing all tables of \code{\link{ICESDatsuscData}}, where column names are included as header rows.
+#' The ICESDatsusc CSV format is a stack of comma separated tables containing all tables of \code{\link{ICESDatsuscData}}, where column names are included as header rows. The file format does not contain the same number of elements in all rows, as the different tables are not padded with columns to produce a regular table. For this reason the output of \code{\link{WriteICESDatsusc}} is a character vector of comma separated strings representing the rows of the \code{\link{ICESDatsuscData}}. The resulting output file written by RstoxFramework can for this reason not be read easily by e.g. \code{\link[data.table]{fread}}.
 #' 
 #' @seealso \code{\link{DataTypes}} for a list of all StoX data types produced by \code{\link{RstoxData}}
 #'