Merge pull request #11 from esqLABS/develop

Merge develop

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: esqlabsRLegacy
 Title: esqLABS utilities package legacy functions
-Version: 3.0.0
+Version: 3.0.1
 Authors@R: 
     c(person("esqLABS GmbH", role = c("cph", "fnd")),
       person("Pavel", "Balazki", role = c("cre", "aut"), email = "pavel.balazki@esqlabs.com"),
@@ -30,4 +30,4 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.1

NEWS.md

@@ -1,3 +1,10 @@
+# esqlabsRLegacy 3.0.1
+
+Fixes unit conversion error when trying to plot data with geometric standard 
+deviation.
+
+-----
+
 # esqlabsRLegacy 3.0.0
 
 - Initial release of the package.

R/DataMapping.R

@@ -499,6 +499,10 @@ DataMapping <- R6::R6Class(
         label <- dataSet$name
         # Create a `XYData` object from `DataSet`
         xyData <- XYData$new(xVals = dataSet$xValues, yVals = dataSet$yValues, yError = dataSet$yErrorValues, label = label)
+        # Check if error type is set in the DataSet object
+        if (!is.null(dataSet$yErrorType)){
+          xyData$yErrorType <- dataSet$yErrorType
+        }
         xyData$dataType <- XYDataTypes$Observed
         xyData$MW <- dataSet$molWeight
         xyData$xDimension <- dataSet$xDimension

R/XYData.R

@@ -165,6 +165,20 @@ XYData <- R6::R6Class(
       }
     },
 
+    #' @field yErrorType Type of error values - either 'ArithmeticStdDev' (default)
+    #' or 'GeometricStdDev'
+    yErrorType = function(value){
+      if (missing(value)) {
+        private$.yErrorType
+      } else {
+        if (!(value %in% c("ArithmeticStdDev", "GeometricStdDev"))){
+          stop("Supported error types are 'ArithmeticStdDev' and 'GeometricStdDev'.")
+        }
+
+        private$.yErrorType <- value
+      }
+    },
+
     #' @field MW Molecular weight in g/mol. Required for conversion between
     #'   molar and mass dimensions. Can be `NULL` (default)
     MW = function(value) {
@@ -186,6 +200,7 @@ XYData <- R6::R6Class(
     .yDimension = NULL,
     .yUnit = NULL,
     .yErrorUnit = NULL,
+    .yErrorType = NULL,
     .MW = NULL,
     .metaData = list()
   ),
@@ -215,6 +230,8 @@ XYData <- R6::R6Class(
 
       self$xDimension <- ospDimensions$Time
       self$yDimension <- ospDimensions$Dimensionless
+
+      private$.yErrorType <- "ArithmeticStdDev"
     },
 
     #' @description Returns the minimal value (minus error, if specified) of the y series that is not negative or null
@@ -280,7 +297,9 @@ XYData <- R6::R6Class(
     },
 
     #' @description
-    #' y error values with all conversions applied.
+    #' y error values with all conversions applied. If error type is 'GeometricStdDev',
+    #' raw error values are multiplied by processed yValues
+    #'
     #'
     #' @param unit Target unit. If `NULL` (default), the no conversion between
     #'   units is applied.
@@ -293,6 +312,10 @@ XYData <- R6::R6Class(
         return(NULL)
       }
 
+      if (private$.yErrorType == "GeometricStdDev"){
+        return(private$.yError * self$yValuesProcessed(unit))
+      }
+
       # Add offset and multiply by the factor. The values are in the unit of XYData
       valuesProcessed <- private$.yError * self$yFactor
 

R/messages.R

@@ -27,3 +27,7 @@ messages$errorWrongLength <- function(object, length, optionalMessage = NULL) {
 messages$errorMultipleMetaDataEntries <- function(optionalMessage = NULL) {
   paste("Can only set a single meta data entry at once", optionalMessage)
 }
+
+messages$dataMappingNoGrouping <- function(optionalMessage = NULL) {
+  paste("No data sets are grouped in the data mapping!", optionalMessage)
+}

R/utilities-data-mapping.R

@@ -393,6 +393,12 @@ plotTimeValues <- function(dataMapping, aggregated, ...) {
 #' @export
 plotPredictedVsObserved <- function(dataMapping, foldDistance = 2, timeDiffThreshold = 10, ...) {
   validateIsOfType(dataMapping, "DataMapping")
+
+  # Cannot create such a plot if no grouping exists
+  if (length(dataMapping$groupings) == 0){
+    stop(messages$dataMappingNoGrouping())
+  }
+
   legendEntries <- c()
   legendColors <- c()
   legendPch <- c()