Merge branch 'develop' into 1261_utf8

Open-Systems-Pharmacology · Sep 6, 2024 · 7371e16 · 7371e16
2 parents 8d1b9bd + 252a166
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diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,9 @@
 
 ## New features
 
+> [!NOTE]
+> Users can now check out [Reporting Engine Test Reports](https://github.com/Open-Systems-Pharmacology/RE-Test-Reports) and access a bunch of template workflows including their R code, models, data and corresponding reports.
+
 - Demography task received significant updates:
    - The [article for demography](../articles/demography.html) has been updated with more comprehensive examples using more representative virtual populations and illustrating the effects of population workflows and settings (#1095, #1102)
    - Categorical parameters, such as Gender, are now accounted for demography range plots and displayed as boxplots (#1088)
@@ -11,10 +14,11 @@
    - Mass balance plots can leverage user-defined settings from json files as illustrated in the [mass balance article](../articles/mass-balance.html) (#1118)
    - Normalized mass balance plots now use time-dependent cumulative drug mass for normalization (#1039, #1118)
 - Qualification DDI plots received the following improvements
-   - Delta symbol (&delta;) from Guest *et al.* formula is indicated in table caption (1069)
+   - Delta symbol (&delta;) from Guest *et al.* formula is indicated in table caption (#1069)
    - Guest criterion (&delta;) can be tuned through the configuration plan (#789)
    - DDI plot format is quadratic by default (#1051)
 - Formatting to word reports can translate additional `html` tags (#382)
+- Goodness of Fit task leverages `groupID` from `Output` objects to group multiple outputs in same time profile and residual plots (#1188).<br>`groupID` is also leveraged in the plots of residuals across the simulations (#1251).
 
 ## Minor improvements and bug fixes
 
@@ -23,6 +27,7 @@
 - Number of bins in demography and PK parameter range plots is consistent with input (#1128)
 - Link/bookmark targets in word reports are better placed (#1084)
 - Qualification time profiles work when no observed data is contained (#1082)
+- Qualification PKRatio uses *ml/min/kg* as default clearance - *CL* - unit (#1242)
 - Static images in qualification reports are better handled (#955, #1071)
 - Figure captions are displayed below the figure in the reports (#1053)
 - Word report is updated if it already existed (#1055)

diff --git a/R/captions.R b/R/captions.R
@@ -36,18 +36,18 @@ captions <- list(
   ),
   demography = list(
     parameterSection = function(sectionId, parameterName) {
-      paste("##", parameterName, "distributions", anchor(sectionId))
+      paste("## ", parameterName, " distributions", anchor(sectionId), sep = "")
     },
     xParameterSection = function(sectionId, parameterName) {
-      paste("## ", parameterName, "-dependence ", anchor(sectionId), sep = "")
+      paste("## ", parameterName, "-dependence", anchor(sectionId), sep = "")
     },
     yParameterSection = function(sectionId, parameterName) {
-      paste("###", parameterName, anchor(sectionId))
+      paste("### ", parameterName, anchor(sectionId), sep = "")
     },
     populationSection = function(sectionId, simulationSetName, descriptor, level = 4) {
       tagLevel <- paste0(rep("#", level), collapse = "")
       sectionTitle <- paste(tagLevel, "For", reportSimulationSet(simulationSetName, descriptor))
-      return(paste(sectionTitle, anchor(sectionId)))
+      return(paste(sectionTitle, anchor(sectionId), sep = ""))
     },
     histogramLegend = function(data, observed = FALSE) {
       if (observed) {
@@ -163,10 +163,10 @@ captions <- list(
       paste0("PK parameters for ", reportSimulationSet(simulationSetName, descriptor))
     },
     outputSection = function(pathName, pathID) {
-      paste("## PK Parameters of", pathName, anchor(pathID))
+      paste("## PK Parameters of ", pathName, anchor(pathID), sep = "")
     },
     parameterSection = function(parameterName, parameterID) {
-      paste("###", parameterName, anchor(parameterID))
+      paste("### ", parameterName, anchor(parameterID), sep = "")
     },
     boxplot = function(parameterName, pathName, simulationSetName, descriptor, plotScale = "linear") {
       paste(
@@ -324,19 +324,22 @@ getTimeRangeCaption <- function(timeRangeName, reference, simulationSetName) {
   if (isIncluded(timeRangeName, ApplicationRanges$total)) {
     return(paste(
       "### For total simulation time range",
-      anchor(paste0(reference, "-", removeForbiddenLetters(simulationSetName), "-", "total"))
+      anchor(paste0(reference, "-", removeForbiddenLetters(simulationSetName), "-", "total")),
+      sep = ""
     ))
   }
   if (isIncluded(timeRangeName, ApplicationRanges$firstApplication)) {
     return(paste(
       "### For first application range",
-      anchor(paste0(reference, "-", removeForbiddenLetters(simulationSetName), "-", "first"))
+      anchor(paste0(reference, "-", removeForbiddenLetters(simulationSetName), "-", "first")),
+      sep = ""
     ))
   }
   if (isIncluded(timeRangeName, ApplicationRanges$lastApplication)) {
     return(paste(
       "### For last application range",
-      anchor(paste0(reference, "-", removeForbiddenLetters(simulationSetName), "-", "last"))
+      anchor(paste0(reference, "-", removeForbiddenLetters(simulationSetName), "-", "last")),
+      sep = ""
     ))
   }
 }

diff --git a/R/configuration-plan.R b/R/configuration-plan.R
@@ -70,7 +70,7 @@ ConfigurationPlan <- R6::R6Class(
       # Issue #1084: new reference title get anchor at the end of title
       addTextChunk(
         fileName = self$getSectionMarkdown(id),
-        text = paste(self$getSectionTitle(id), anchor(sectionReference))
+        text = paste(self$getSectionTitle(id), anchor(sectionReference), sep = "")
       )
       # Add section content
       sectionContent <- private$.sections$content[selectedId]

diff --git a/R/error-checks.R b/R/error-checks.R
@@ -669,25 +669,25 @@ checkSamePopulationIds <- function(setIds,
 #' @keywords internal
 checkMetaDataIsConsistent <- function(metaData) {
   groupId <- unique(metaData$group)
-  if(!isOfLength(unique(metaData$unit), 1)){
+  if (!isOfLength(unique(metaData$unit), 1)) {
     warning(
       messages$inconsistentMetaData(
-        values = metaData$unit, 
-        id = groupId, 
+        values = metaData$unit,
+        id = groupId,
         dataType = "units"
-        ),
+      ),
       call. = FALSE
-      )
+    )
   }
-  if(!isOfLength(unique(metaData$residualScale), 1)){
+  if (!isOfLength(unique(metaData$residualScale), 1)) {
     warning(
       messages$inconsistentMetaData(
-        values = metaData$residualScale, 
-        id = groupId, 
+        values = metaData$residualScale,
+        id = groupId,
         dataType = "residualScale"
       ),
       call. = FALSE
     )
   }
   return()
-}
+}
diff --git a/R/gof-plot-task.R b/R/gof-plot-task.R
@@ -15,8 +15,9 @@ GofPlotTask <- R6::R6Class(
       addTextChunk(
         fileName = self$fileName,
         text = paste(
-          "##", self$title, "for", simulationSetName,
-          anchor(paste0(self$reference, "-", removeForbiddenLetters(simulationSetName)))
+          "## ", self$title, " for ", simulationSetName,
+          anchor(paste0(self$reference, "-", removeForbiddenLetters(simulationSetName))),
+          sep = ""
         )
       )
       for (result in taskResults) {
@@ -76,7 +77,8 @@ GofPlotTask <- R6::R6Class(
         fileName = self$fileName,
         text = paste(
           "## Residuals across all simulations",
-          anchor(paste0(self$reference, "-residuals-across-all-simulations"))
+          anchor(paste0(self$reference, "-residuals-across-all-simulations")),
+          sep = ""
         )
       )
       for (result in taskResults) {
@@ -136,7 +138,7 @@ GofPlotTask <- R6::R6Class(
       resetReport(self$fileName)
       addTextChunk(
         fileName = self$fileName,
-        text = paste("#", self$title, anchor(self$reference))
+        text = paste("# ", self$title, anchor(self$reference), sep = "")
       )
       if (!is.null(self$outputFolder)) {
         dir.create(file.path(self$workflowFolder, self$outputFolder), showWarnings = FALSE)

diff --git a/R/messages.R b/R/messages.R
@@ -255,46 +255,46 @@ messages <- list(
   warningNAFoundInPKAnalysisFile = function(filePath) {
     paste0(highlight("NaN"), " found in PK analysis file '", highlight(filePath), "'.")
   },
-  warningPKAnalysesMissingIds = function(ids, setName){
+  warningPKAnalysesMissingIds = function(ids, setName) {
     paste0(
-      "Missing ", highlight("IndividualIds"), " in PKAnalysis file for simulation set '", 
+      "Missing ", highlight("IndividualIds"), " in PKAnalysis file for simulation set '",
       highlight(setName), "': ",
       paste0("'", highlight(ids), "'", collapse = ", ")
     )
   },
-  warningPKAnalysesMissingIds = function(ids, setName){
+  warningPKAnalysesMissingIds = function(ids, setName) {
     paste0(
-      "Missing ", highlight("IndividualIds"), " in PKAnalysis file for simulation set '", 
+      "Missing ", highlight("IndividualIds"), " in PKAnalysis file for simulation set '",
       highlight(setName), "': ",
       paste0("'", highlight(ids), "'", collapse = ", ")
     )
   },
-  warningMissingFromReferenceSet = function(path, simulationSetName, pkParameters = NULL){
-    if(is.null(pkParameters)){
+  warningMissingFromReferenceSet = function(path, simulationSetName, pkParameters = NULL) {
+    if (is.null(pkParameters)) {
       return(
         paste0(
-          "Output path '", highlight(path), 
-          "' was NOT defined for reference simulation set '", highlight(simulationSetName), 
+          "Output path '", highlight(path),
+          "' was NOT defined for reference simulation set '", highlight(simulationSetName),
           "'. Ouptut path and its PK Parameters were added to the list of figures to export."
         )
       )
     }
     return(
       paste0(
-        "The following PK Parameters '", 
-        paste(highlight(pkParameters), collapse = "', '"), 
-        "' were NOT defined for the Ouptut path '", highlight(path), 
-        "' in the reference simulation set '", highlight(simulationSetName), 
+        "The following PK Parameters '",
+        paste(highlight(pkParameters), collapse = "', '"),
+        "' were NOT defined for the Ouptut path '", highlight(path),
+        "' in the reference simulation set '", highlight(simulationSetName),
         "'. The PK Parameters were added to the list of figures to export."
       )
     )
   },
-  inconsistentMetaData = function(values, id, dataType = "units"){
+  inconsistentMetaData = function(values, id, dataType = "units") {
     paste0(
-      "Inconsistent ", highlight(dataType), 
+      "Inconsistent ", highlight(dataType),
       " found within Group ID '", highlight(id), "': '",
       paste0(highlight(unique(values)), collapse = "', '"), "'."
-      )
+    )
   },
   #----- Info messages ----
   runStarting = function(runName, subRun = NULL) {

diff --git a/R/plot-task.R b/R/plot-task.R
@@ -50,8 +50,9 @@ PlotTask <- R6::R6Class(
       addTextChunk(
         fileName = self$fileName,
         text = paste(
-          "##", self$title, "for", simulationSetName,
-          anchor(paste0(self$reference, "-", removeForbiddenLetters(simulationSetName)))
+          "## ", self$title, " for ", simulationSetName,
+          anchor(paste0(self$reference, "-", removeForbiddenLetters(simulationSetName))),
+          sep = ""
         )
       )
       for (result in taskResults) {
@@ -113,7 +114,7 @@ PlotTask <- R6::R6Class(
       resetReport(self$fileName)
       addTextChunk(
         fileName = self$fileName,
-        text = paste("#", self$title, anchor(self$reference))
+        text = paste("# ", self$title, anchor(self$reference), sep = "")
       )
       if (!is.null(self$outputFolder)) {
         dir.create(file.path(self$workflowFolder, self$outputFolder), showWarnings = FALSE)

diff --git a/R/population-plot-task.R b/R/population-plot-task.R
@@ -38,7 +38,7 @@ PopulationPlotTask <- R6::R6Class(
       resetReport(self$fileName)
       addTextChunk(
         fileName = self$fileName,
-        text = paste("#", self$title, anchor(self$reference))
+        text = paste("# ", self$title, anchor(self$reference), sep = "")
       )
       for (result in taskResults) {
         # Get both absolute and relative paths for figures and tables

diff --git a/R/qualification-ddi.R b/R/qualification-ddi.R
@@ -545,8 +545,10 @@ plotQualificationDDIs <- function(configurationPlan, settings) {
         # Subheading result includes anchor tag to be referenced in TOC
         textChunk = paste(
           paste0(rep("#", sectionLevel + 1), collapse = ""),
+          " ",
           subplotTypeName,
-          anchor(paste0(sectionID, "-ddi-subunit-", length(ddiResults) + 1))
+          anchor(paste0(sectionID, "-ddi-subunit-", length(ddiResults) + 1)),
+          sep = ""
         ),
         includeTextChunk = TRUE
       )
@@ -562,8 +564,10 @@ plotQualificationDDIs <- function(configurationPlan, settings) {
           # Subheading result includes anchor tag to be referenced in TOC
           textChunk = paste(
             paste0(rep("#", sectionLevel + 2), collapse = ""),
+            " ",
             subplotTypeLevel,
-            anchor(paste0(sectionID, "-ddi-subunit-", length(ddiResults) + 1))
+            anchor(paste0(sectionID, "-ddi-subunit-", length(ddiResults) + 1)),
+            sep = ""
           ),
           includeTextChunk = TRUE
         )

diff --git a/R/simulation-set.R b/R/simulation-set.R
@@ -57,7 +57,7 @@ SimulationSet <- R6::R6Class(
       validateIsString(simulationFile)
       validateIsFileExtension(simulationFile, "pkml")
       validateIsUnitFromDimension(timeUnit, "Time")
-      
+
       # For optional input, usually null is allowed
       # but not here as it would mean that nothing would be reported
       validateIsIncluded(c(applicationRanges), ApplicationRanges)
@@ -66,22 +66,22 @@ SimulationSet <- R6::R6Class(
         validateIsFileExtension(massBalanceFile, "json")
         self$massBalanceSettings <- jsonlite::fromJSON(massBalanceFile, simplifyVector = FALSE)[["MassBalancePlots"]]
       }
-      
+
       # Before loading the simulation, check if the file exists
       validateFileExists(simulationFile)
       simulation <- ospsuite::loadSimulation(simulationFile, addToCache = FALSE)
       validateVector(minimumSimulationEndTime, type = "numeric", valueRange = c(0, Inf), nullAllowed = TRUE)
       # Following checks require simulation info
       endTime <- max(
-        minimumSimulationEndTime, 
+        minimumSimulationEndTime,
         ospsuite::toUnit(
           quantityOrDimension = "Time",
           values = simulation$outputSchema$endTime,
           targetUnit = timeUnit
         )
       )
       validateVectorRange(timeOffset, type = "numeric", valueRange = c(0, endTime))
-      
+
       # Test and validate outputs and their paths
       validateOutputObject(c(outputs), simulation, nullAllowed = TRUE)
       validateDataSource(dataSource, c(outputs), nullAllowed = TRUE)

diff --git a/R/utilities-goodness-of-fit.R b/R/utilities-goodness-of-fit.R
@@ -1154,7 +1154,7 @@ getResidualsPlotResultsInGroup <- function(data, metaData, outputId, structureSe
     plotConfiguration = qqPlotConfiguration
   )
   goodnessOfFitCaptions[[resultId$resQQPlot]] <- getGoodnessOfFitCaptions(structureSet, "resQQPlot", residualScale, settings)
-  
+
   return(list(
     plots = goodnessOfFitPlots,
     captions = goodnessOfFitCaptions

diff --git a/R/utilities-mass-balance.R b/R/utilities-mass-balance.R
@@ -37,7 +37,7 @@ plotMeanMassBalance <- function(structureSet, settings = NULL) {
       sectionId <- defaultFileNames$resultID(length(massBalanceResults) + 1, "mass_balance")
       massBalanceResults[[sectionId]] <- saveTaskResults(
         id = sectionId,
-        textChunk = paste("###", plotSettings$Name, anchor(sectionId)),
+        textChunk = paste("### ", plotSettings$Name, anchor(sectionId), sep = ""),
         includeTextChunk = TRUE
       )
     }