478 lloq legend (#1048)

* Fixes #478 indicate lloq in time profiles

* Fixes #478 lloq dotted lines appear on plots

* Enforce missing lloq as numeric class preventing ggplot scale issues

* Update documentation now that lloq is handled differently

R/error-checks.R

@@ -459,4 +459,27 @@ validateGuestParameters <- function(guestParameters, pkParameters) {
       }
     )
   return(invisible())
-}
+}
+
+checkLLOQValues <- function(lloq, structureSet){
+  if(any(is.infinite(lloq))){
+    warning(
+      messages$warningHasInfiniteValues(
+        n = sum(is.infinite(lloq)),
+        datasetName = structureSet$simulationSet$dataSource$dataFile
+        ),
+      call. = FALSE
+      )
+    lloq[is.infinite(lloq)] <- NA
+  }
+  # If no negative value, return lloq
+  if(isEmpty(which(lloq<=0))){
+    return(lloq)
+  }
+  warning(
+    messages$negativeDataRemoved(length(which(lloq<=0))),
+    call. = FALSE
+    )
+  lloq[lloq<=0 & !is.na(lloq)] <- NA
+  return(lloq)
+}

R/gof-plot-task.R

@@ -167,7 +167,7 @@ GofPlotTask <- R6::R6Class(
           self$saveResults(set, taskResults$results)
 
           # If first simulation set was a reference population,
-          # its simulated, observed and lloq data are added for the next plots through settings
+          # its simulated and observed data are added for the next plots through settings
           # the option plotReferenceObsData from the simulation set will take care of the actual inclusion within the plots
           if (all(isTRUE(set$simulationSet$referencePopulation), isTRUE(self$settings$includeReferenceData))) {
             self$settings$referenceData <- taskResults$referenceData

R/messages.R

@@ -224,6 +224,14 @@ messages <- list(
     "Qualification TimeProfile is unable to display data for all 3 axes. Only Y and Y2 axes were kept."
   },
 
+  warningHasInfiniteValues = function(n, datasetName = NULL){
+    paste0(
+      "Data ", 
+      ifNotNull(datasetName, paste0("from '", highlight(datasetName), "' "), ""),
+      "included ", highlight(n), " infinite values"
+    )
+  },
+
   pkParameterNotFound = function(pkParameterName, pkRatioMapping){
     paste0(
       "PK Parameter '", highlight(pkParameterName), "' not found for ",

R/qualification-gof.R

@@ -149,9 +149,12 @@ getGOFDataForMapping <- function(outputMapping, configurationPlan, axesUnits) {
     )
 
     # Re-use nomenclature and functions from utilities-goodness-of-fit
+    # TODO: Qualification currently do not handle LLOQ
+    # Add place holder for lloq, that will be replaced once data include lloq information
     observedData <- data.frame(
       Time = observedTime,
       Concentration = observedValues,
+      lloq = as.numeric(NA),
       Path = observedDataSet
     )
     simulatedData <- data.frame(