Fixes Open-Systems-Pharmacology#876 introduce default statistics Fixes …

…Open-Systems-Pharmacology#875 superscript th

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+export("geomean*sd")
+export("geomean/sd")
 export(AggregationConfiguration)
 export(AllAvailableTasks)
 export(ApplicationRanges)
@@ -23,6 +25,7 @@ export(SensitivityPlotSettings)
 export(SimulationSet)
 export(StandardPlotTasks)
 export(StandardSimulationTasks)
+export(StatisticsTypes)
 export(Task)
 export(activateWorkflowTasks)
 export(addFigureChunk)
@@ -57,6 +60,7 @@ export(defaultSimulationNumberOfCores)
 export(defaultVariationRange)
 export(evalDataFilter)
 export(generateResultFileNames)
+export(geomean)
 export(getAnchorName)
 export(getDefaultDemographyXParameters)
 export(getDefaultPKParametersXParameters)
@@ -74,6 +78,7 @@ export(getResiduals)
 export(getSimulationDescriptor)
 export(getSimulationParameterDisplayPaths)
 export(getSimulationResultFileNames)
+export(getStatisticsFromType)
 export(getTaskInputs)
 export(getWorkflowParameterDisplayPaths)
 export(getXParametersForDemogrpahyPlot)
@@ -117,7 +122,9 @@ export(plotMassBalanceCumulativeTimeProfile)
 export(plotMassBalancePieChart)
 export(plotMassBalanceTimeProfile)
 export(plotMeanTimeProfile)
+export(plotMeanTimeProfileLog)
 export(plotPopulationTimeProfile)
+export(plotPopulationTimeProfileLog)
 export(prettyCaption)
 export(ratioBoxplot)
 export(readObservedDataFile)
@@ -135,6 +142,7 @@ export(setDefaultPlotFormat)
 export(setDefaultStairstep)
 export(setDefaultTheme)
 export(setDefaultThemeFromJson)
+export(setDefaultTimeProfileStatistics)
 export(setPlotFormat)
 export(setSimulationDescriptor)
 export(setWatermarkConfiguration)

R/messages.R

@@ -277,6 +277,9 @@ messages <- list(
   },
   completedOnCores = function(objectNames) {
     paste0(objectNames, " successfully completed on all cores")
+  },
+  negativeDataRemoved = function(n) {
+    paste0(n, " negative or null values were removed from logarithmic plot")
   }
 )
 

R/reportingengine-env.R

@@ -97,7 +97,6 @@ reEnv$ddiRatioSubsetsDictionary <- list(
 # Default value for a scale factor used in a parallel simulation.  The product of this scale factor and the number of allowable cores (allowedCores) sets the maximum number of simulations that may be run on one core.
 reEnv$defaultMaxSimulationsPerCore <- 2
 
-
 #' @title setWatermarkConfiguration
 #' @description Set default watermark configuration for current theme
 #' @param watermark character or \code{Label} class object from `tlf` package
@@ -250,3 +249,132 @@ setDefaultAutoAxisLimitMargin <- function(margin) {
   validateIsNumeric(margin)
   reEnv$autoAxisLimitMargin <- margin
 }
+
+#' @title StatisticsTypes
+#' @description List of available statistic types summarizing data for time profile plots
+#' \itemize{
+#' \item `"2.5th-97.5th Percentiles"` summarizes data using median, 2.5th and 97.5th percentiles
+#' \item `"5th-95th Percentiles"` summarizes data using median, 5th and 95th percentiles
+#' \item `"10th-90th Percentiles"` summarizes data using median, 10th and 90th percentiles
+#' \item `"Geometric mean"` summarizes data using geometric mean and mean */ geometric standard deviation
+#' \item `"Arithmetic mean"` summarizes data using arithmetic mean and mean +/- standard deviation
+#' }
+#' 
+#' @export
+#' @family enum helpers
+#' @examples dontrun{
+#' getStatisticsFromType(StatisticsTypes)
+#' }
+StatisticsTypes <- enum(c(
+  "2.5th-97.5th Percentiles",
+  "5th-95th Percentiles",
+  "10th-90th Percentiles",
+  "Geometric mean",
+  "Arithmetic mean"
+))
+
+
+#' @title getStatisticsFromType
+#' @description Get statistics 
+#' @param statisticsType Statistics summarizing time profile simulated data
+#' as defined by helper enum `StatisticsType`
+#' @return A list including `y`, `ymin` and `ymax` summary statistics as well as their `caption`
+#' @export
+#' @examples dontrun{
+#' workflow$plotTime
+#' }
+getStatisticsFromType <- function(statisticsType){
+  validateIsIncluded(statisticsType, StatisticsTypes)
+  if(isIncluded(statisticsType, StatisticsTypes$`2.5th-97.5th Percentiles`)){
+    return(list(
+      y = tlf::tlfStatFunctions$`Percentile50%`,
+      ymin = tlf::tlfStatFunctions$`Percentile2.5%`,
+      ymax = tlf::tlfStatFunctions$`Percentile97.5%`,
+      yCaption = "median",
+      # The unicode characters below are superscript th
+      rangeCaption = "[2.5\u1d57\u02b0-97.5\u1d57\u02b0] percentiles"
+    ))
+  }
+  if(isIncluded(statisticsType, StatisticsTypes$`5th-95th Percentiles`)){
+    return(list(
+      y = tlf::tlfStatFunctions$`Percentile50%`,
+      ymin = tlf::tlfStatFunctions$`Percentile5%`,
+      ymax = tlf::tlfStatFunctions$`Percentile95%`,
+      yCaption = "median",
+      rangeCaption = "[5\u1d57\u02b0-95\u1d57\u02b0] percentiles"
+    ))
+  }
+  if(isIncluded(statisticsType, StatisticsTypes$`10th-90th Percentiles`)){
+    return(list(
+      y = tlf::tlfStatFunctions$`Percentile50%`,
+      ymin = tlf::tlfStatFunctions$`Percentile10%`,
+      ymax = tlf::tlfStatFunctions$`Percentile90%`,
+      yCaption = "median",
+      rangeCaption = "[10\u1d57\u02b0-90\u1d57\u02b0] percentiles"
+    ))
+  }
+  if(isIncluded(statisticsType, StatisticsTypes$`Arithmetic mean`)){
+    return(list(
+      y = tlf::tlfStatFunctions$mean,
+      ymin = tlf::tlfStatFunctions$`mean-sd`,
+      ymax = tlf::tlfStatFunctions$`mean+sd`,
+      yCaption = "arithmetic mean",
+      # The unicode character below is +/- symbol
+      rangeCaption = "mean \u00b1 SD range"
+    ))
+  }
+  #TODO : define geometric mean in tlf !
+  return(list(
+    y = "geomean",
+    ymin = "geomean/sd",
+    ymax = "geomean*sd",
+    yCaption = "geometric mean",
+    # The unicode character below is supposed to be */ symbol
+    rangeCaption = "mean \u22c7 geometric SD range"
+  ))
+}
+
+reEnv$defaultTimeProfileStatistics <- getStatisticsFromType(StatisticsTypes$`5th-95th Percentiles`)
+
+#' @title setDefaultTimeProfileStatistics
+#' @description Set default statistics used in population time profiles and residuals plots
+#' @param statisticsType Name of statistics type as defined in enum `StatisticsTypes`
+#' @param y Function or function name for middle values statistics
+#' @param ymin Function or function name for min values statistics
+#' @param ymax Function or function name for max values statistics
+#' @param yCaption Legend caption for middle values statistics
+#' @param rangeCaption Legend caption for range values statistics
+#' @export
+#' @examples \dontrun{
+#' # Set the default statistics as geometric mean
+#' setDefaultTimeProfileStatistics(statisticsType = StatisticsTypes$`Geometric mean`)
+#' 
+#' # Set the default legend caption displayed for range
+#' setDefaultTimeProfileStatistics(rangeCaption = "90% population range")
+#' 
+#' }
+#' 
+setDefaultTimeProfileStatistics <- function(statisticsType = NULL,
+                                            y = NULL, 
+                                            ymin = NULL, 
+                                            ymax = NULL, 
+                                            yCaption = NULL,
+                                            rangeCaption = NULL){
+
+  validateIsIncluded(statisticsType, StatisticsTypes, nullAllowed = TRUE)
+  # Allow user to enter the function directly
+  validateIsOfType(y, c("character", "closure"), nullAllowed = TRUE)
+  validateIsOfType(ymin, c("character", "closure"), nullAllowed = TRUE)
+  validateIsOfType(ymax, c("character", "closure"), nullAllowed = TRUE)
+
+  if(!isEmpty(statisticsType)){
+    reEnv$defaultTimeProfileStatistics <- getStatisticsFromType(statisticsType)
+  }
+  # Assign variables to reEnv only if defined
+  eval(parseVariableToObject(
+    objectName = "reEnv$defaultTimeProfileStatistics",
+    variableName = c("y", "ymin", "ymax", "yCaption", "rangeCaption"),
+    keepIfNull = TRUE))
+
+  return(invisible())
+}

R/task-settings.R

@@ -4,6 +4,8 @@
 #' @keywords internal
 TaskSettings <- R6::R6Class(
   "TaskSettings",
+  # This allows the R6 class to accept new fields
+  lock_objects = FALSE,
   public = list(
     #' @description
     #' Create a `TaskSettings` object
@@ -147,18 +149,83 @@ GofTaskSettings <- R6::R6Class(
   public = list(
     #' @field referenceData Data results obtained by TimeProfilesAndResiduals task corresponding to referencePopulation
     referenceData = NULL,
-
+    
     #' @description
     #' Create a `GofTaskSettings` object
     #' @param taskName name of the task using the settings
     #' @param outputSelections subset of simulationSet outputs to be used in GoF plot
+    #' @param statisticsType Statistics summarizing time profile simulated data
     #' @return A new `GofTaskSettings` object
-    initialize = function(taskName = AllAvailableTasks$plotTimeProfilesAndResiduals, outputSelections = NULL) {
+    initialize = function(taskName = AllAvailableTasks$plotTimeProfilesAndResiduals, 
+                          outputSelections = NULL,
+                          statisticsType = NULL) {
       validateIsIncluded(taskName, AllAvailableTasks$plotTimeProfilesAndResiduals)
+      validateIsIncluded(statisticsType, StatisticsTypes, nullAllowed = TRUE)
+
       super$initialize(taskName)
+
       private$.includeReferenceData <- TRUE
       private$.outputSelections <- outputSelections
+      private$.statistics <- reEnv$defaultTimeProfileStatistics
+      self$setStatistics(statisticsType = statisticsType)
+
+    },
+
+    #' @description Set statistics used in population time profiles and residuals plots
+    #' @param statisticsType Name of statistics type as defined in enum `StatisticsTypes`
+    #' @param y Function or function name for middle values statistics
+    #' @param ymin Function or function name for min values statistics
+    #' @param ymax Function or function name for max values statistics
+    #' @param yCaption Legend caption for middle values statistics
+    #' @param rangeCaption Legend caption for range values statistics
+    #' @examples \dontrun{
+    #' # Set the statistics as geometric mean
+    #' workflow$plotTimeProfilesAndResiduals$settings$setStatistics(
+    #' statisticsType = StatisticsTypes$`Geometric mean`
+    #' )
+    #' 
+    #' # Set the legend caption displayed for range
+    #' workflow$plotTimeProfilesAndResiduals$settings$setStatistics(
+    #' statisticsType = StatisticsTypes$`Geometric mean`
+    #' rangeCaption = "90% population range"
+    #' )
+    #' 
+    #' }
+    #' 
+    setStatistics = function(statisticsType = NULL,
+                              y = NULL, 
+                              ymin = NULL, 
+                              ymax = NULL, 
+                              yCaption = NULL,
+                              rangeCaption = NULL){
+
+      validateIsIncluded(statisticsType, StatisticsTypes, nullAllowed = TRUE)
+      # Allow user to enter the function directly
+      validateIsOfType(y, c("character", "closure"), nullAllowed = TRUE)
+      validateIsOfType(ymin, c("character", "closure"), nullAllowed = TRUE)
+      validateIsOfType(ymax, c("character", "closure"), nullAllowed = TRUE)
+
+      if(!isEmpty(statisticsType)){
+        private$.statistics <- getStatisticsFromType(statisticsType)
+      }
+      # Assign variables to reEnv only if defined
+      eval(parseVariableToObject(
+        objectName = "private$.statistics",
+        variableName = c("y", "ymin", "ymax", "yCaption", "rangeCaption"),
+        keepIfNull = TRUE))
+      return(invisible())
+    },
+
+    #' @description Get statistics used in population time profiles and residuals plots
+    #' @examples \dontrun{
+    #' # Get the statistics of time profiles task
+    #' workflow$plotTimeProfilesAndResiduals$settings$getStatistics()
+    #' }
+    #' 
+    getStatistics = function(){
+      return(private$.statistics)
     }
+
   ),
   active = list(
     #' @field includeReferenceData logical defining if reference population should be included in
@@ -181,9 +248,11 @@ GofTaskSettings <- R6::R6Class(
       private$.outputSelections <- value %||% private$.outputSelections
       return(invisible())
     }
+
   ),
   private = list(
     .includeReferenceData = NULL,
-    .outputSelections = NULL
+    .outputSelections = NULL,
+    .statistics = NULL
   )
 )