Improved error when CVVariable is not given in PlotReportBootstrap()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: RstoxFramework
 Version: 4.2.1
-Date: 2026-06-26
+Date: 2026-07-06
 Title: The Engine of StoX
 Authors@R: c(
   person(given = "Arne Johannes", 

NEWS.md

@@ -1,3 +1,8 @@
+# RstoxFramework v4.2.1 (2025-07-04)
+* Improved error when CVVariable is not given in PlotReportBootstrap().
+* Added support for an actual function in replaceData in runProcess() and replaceDataList in runModel(), runProject() and runProjects().
+
+
 # RstoxFramework v4.2.1-9005 (2025-06-13)
 * Fixed bug in zipProject(), where large files failed, presumably due to the q flag, which is now removed.
 

R/Framework.R

@@ -5814,18 +5814,41 @@ runProcess <- function(
 
     # Apply the replaceData, which can be a function with first parameter the processOutput and additional parameters given in ..., or an actual object to replace the output by:
     #thisReplaceData <- replaceData[[process$processName]]
-    if(length(replaceData) && is.character(replaceData)) {
-        replaceData <- list(FunctionName = replaceData)
+    if(length(replaceData) == 1) {
+        if(is.character(replaceData)) {
+            replaceData <- list(FunctionName = replaceData)
+        }
+        else if(is.function(replaceData)) {
+            replaceData <- list(FunctionName = replaceData)
+        }
     }
-    if(is.list(replaceData) && !data.table::is.data.table(replaceData) && is.character(replaceData$FunctionName)) {
+
+    # Check whether the replaceData has a function in FunctionName:
+    replaceData_hasFunction <- 
+        # A list:
+        is.list(replaceData) && !data.table::is.data.table(replaceData) && 
+        # ... and
+        ( 
+            # a string naming a function:
+            is.character(replaceData$FunctionName) || 
+            # ... or a function:
+            is.function(replaceData$FunctionName)
+        )
+
+    if(replaceData_hasFunction) {
 
         # Add a message when replacing data using a function:
         message(
             "StoX: Replacing data in ", modelName, " process ", 
             getProcessIndexFromProcessID(projectPath = projectPath, modelName = modelName, processID = processID), 
             ": ", 
             getProcessName(projectPath = projectPath, modelName = modelName, processID = processID), 
-            " using the function ", replaceData$FunctionName, ".",
+            if(is.function(replaceData$FunctionName)) 
+                " using the function given by replaceData$FunctionName"
+            else 
+                paste0(" using the function ", replaceData$FunctionName, 
+            "."),
+
             appendLF = TRUE
         )
 
@@ -5872,6 +5895,8 @@ runProcess <- function(
         processOutput <- replaceData
     }
 
+
+
     # Clear memory to avoid memory leak when running parallel bootstrapping. NEVER remove this unless the performance has been thoroughly tested by running bootstrap on multiple large StoX projects sequentially, to give R a chance to pile up memory:
     #gc()
 
@@ -5890,7 +5915,7 @@ runProcess <- function(
             currentActiveProcessID = currentActiveProcessID, 
             processDirty = FALSE
         )
-
+    
         # If a valid output class, wrap the function output to a list named with the data type:
         if(isValidOutputDataClass(processOutput)) {
             processOutput <- list(processOutput)
@@ -5919,7 +5944,6 @@ runProcess <- function(
             writeActiveProcessID(projectPath, modelName, propertyDirty = FALSE)
         }
 
-
         # Write to memory files. Here we pass processOutput as input and get the processOutput as output, since in the case that the processOutput is a file path to a temporary NewCDF4 file (only relevant for the Bootstrap function for now) the file is copied to the projectSession folder and an attribute added to the file name:
         processOutput <- writeProcessOutputMemoryFiles(processOutput = processOutput, projectPath = projectPath, modelName = modelName, processID = process$processID)
 
@@ -7215,7 +7239,7 @@ writeStoxOutputOne <- function(processOutputOne, filePath, escape = TRUE) {
                 writeGPX_track_points(processOutputOne, filePath)
             }
             else {
-                writeGPX_waypoints(processOutputOne, filePath)
+                writeGPX_waypoint(processOutputOne, filePath)
             }
 
         }
@@ -7312,7 +7336,7 @@ writeGPX_track_points <- function(
 }
 
 
-writeGPX_waypoints <- function(
+writeGPX_waypoint <- function(
     x, 
     filePath, 
     layers = c("geometry", "Stratum", "name")
@@ -7331,6 +7355,27 @@ writeGPX_waypoints <- function(
 }
 
 
+writeGPX_route_layer <- function(
+        x, 
+        filePath, 
+        layers = c("geometry", "name")
+) {
+
+    # Keep only the specified layers:
+    x <- subset(x, select = layers)
+
+    sf::st_write(
+        x,
+        dsn = filePath,
+        layer = "route_layer",
+        driver = "GPX", 
+        dataset_options = "GPX_USE_EXTENSIONS=YES"
+    )
+}
+
+
+
+
 ggsaveApplyDefaults <- function(x, filePath, overrideAttributes = list()) {
 
     # Replace any attributes given in the overrideAttributes:

R/Plot.R

@@ -212,6 +212,12 @@ PlotReportBootstrapOne <- function(plotArguments, ind = NULL) {
 
     maxPlottingVariable <- plotArguments$ReportBootstrapData[, max(get(plotArguments$PlottingVariableUpper), na.rm = TRUE)]
     if(plotArguments$AddCVToPlot) {
+
+        # Error if the plotArguments$CVVariable is not given:
+        if(!length(plotArguments$CVVariable) || (length(plotArguments$CVVariable) && !nchar(plotArguments$CVVariable))) {
+            stop("The CVVariable is not given.")
+        }
+
         maxCV <- plotArguments$ReportBootstrapData[, max(get(plotArguments$CVVariable), na.rm = TRUE)]
         cvScalingFactor <- maxPlottingVariable / maxCV
         plotArguments$ReportBootstrapData[, eval(plotArguments$CVVariable) := get(plotArguments$CVVariable) * cvScalingFactor]

R/resample.R

@@ -688,7 +688,7 @@ readBootstrapDataOne <- function(selectionOneTable, nc, BootstrapID = NA) {
     varListFullName <- unname(unlist(lapply(varList, function(x) lapply(x, function(y) apply(y, 1, paste, collapse = "/")))))
     notPresentInFile <- setdiff(requestedVariablesFullName, varListFullName)
     if(length(notPresentInFile)) {
-        stop("The following requested variables are not present in the file ", nc$filename, " (These variables can be added using the parameter OutputVariables of the function Bootstrap()): \n", paste(notPresentInFile, collapse = "\n"))
+        stop("The following requested variables are not present in the file ", nc$filename, " (These variables can be added using the parameter OutputVariables of the function Bootstrap(), or the function getOutputVariablesUsedInReport can be used to get a full list of required OutputVariables): \n", paste(notPresentInFile, collapse = "\n"))
     }
 
     # Get the nrow variable, which determines what to read, and which will be added as BootstrapID to the output table:

inst/versions/OfficialRstoxFrameworkVersions.txt

@@ -102,4 +102,4 @@ StoX	RstoxFramework	Dependencies	OptionalDependencies	Official	Date
 4.2.1-9003	4.2.1-9004	RstoxBase_2.2.1-9003,RstoxData_2.2.1-9005	RstoxFDA_1.7.0-9999	FALSE	2026-05-22
 4.2.1-9004	4.2.1-9005	RstoxBase_2.2.1-9005,RstoxData_2.2.1-9007	RstoxFDA_1.7.0-9999	FALSE	2026-06-13
 4.2.1-9005	4.2.1-9006	RstoxBase_2.2.1-9006,RstoxData_2.2.1-9008	RstoxFDA_1.7.0-9999	FALSE	2026-06-23
-4.2.1	4.2.1	RstoxBase_2.2.1,RstoxData_2.2.1	RstoxFDA_1.7.0	TRUE	2026-06-26
+4.2.1	4.2.1	RstoxBase_2.2.1,RstoxData_2.2.1	RstoxFDA_1.7.0	TRUE	2026-07-06