diff --git a/R/gof-plot-task.R b/R/gof-plot-task.R
index d1e00f41..8b84a219 100644
--- a/R/gof-plot-task.R
+++ b/R/gof-plot-task.R
@@ -178,9 +178,13 @@ GofPlotTask <- R6::R6Class(
if (isEmpty(taskResults[["residuals"]])) {
next
}
- residualsInSimulation <- taskResults$residuals$data
- residualsMetaData <- taskResults$residuals$metaData
- residualsInSimulation$Legend <- set$simulationSet$simulationSetName
+ residualsInSimulation <- taskResults$residuals
+ # Update residuals data for residuals accross all simulations
+ residualsInSimulation$Legend <- reportSimulationSet(
+ simulationSetName = set$simulationSet$simulationSetName,
+ descriptor = set$simulationSetDescriptor
+ )
+
residualsAcrossAllSimulations <- rbind.data.frame(
residualsAcrossAllSimulations,
residualsInSimulation
@@ -188,7 +192,13 @@ GofPlotTask <- R6::R6Class(
}
}
- if (isEmpty(residualsAcrossAllSimulations)) {
+ # Conditions where residuals across all simulations are not reported
+ noResidualsAcrossAllSimulations <- any(
+ isOfLength(structureSets, 1),
+ isEmpty(residualsAcrossAllSimulations)
+ )
+
+ if (noResidualsAcrossAllSimulations) {
re.tEndAction(actionToken = actionToken)
logInfo(messages$runCompleted(getElapsedTime(t0), self$message))
return(invisible())
@@ -197,7 +207,6 @@ GofPlotTask <- R6::R6Class(
residualsResults <- self$getResidualsResults(
structureSets = structureSets,
data = residualsAcrossAllSimulations,
- metaData = residualsMetaData,
settings = self$settings
)
self$saveResidualsResults(residualsResults)
@@ -210,10 +219,9 @@ GofPlotTask <- R6::R6Class(
#' Get plot results for residuals across all simulations
#' @param structureSets A list of `SimulationStructure` objects defining the properties of a simulation set
#' @param data data.frame
- #' @param metaData meta data on `data`
#' @param settings List of settings such as `PlotConfiguration` R6 class objects for each goodness of fit plot
#' @return A list of `TaskResults` objects
- getResidualsResults = function(structureSets, data, metaData, settings) {
+ getResidualsResults = function(structureSets, data, settings) {
residualsResults <- list()
simulationSetNames <- sapply(structureSets, function(set) {
set$simulationSet$simulationSetName
@@ -230,57 +238,246 @@ GofPlotTask <- R6::R6Class(
includeTable = FALSE
)
- # Plot the residuals across the simulations
- resultID <- defaultFileNames$resultID(
- "residuals-across-all-simulations-histogram"
- )
-
- residualsHistogramPlot <- tlf::plotHistogram(
- data = data,
- metaData = metaData,
- dataMapping = tlf::HistogramDataMapping$new(
- x = "Residuals",
- fill = "Legend",
- stack = TRUE,
- distribution = "normal"
- ),
- plotConfiguration = settings$plotConfigurations[["histogram"]],
- bins = settings$bins %||% reEnv$defaultBins
+ # Get all unique output paths
+ # TODO: group them by unique ID once introduced
+ allOutputs <- sapply(
+ structureSets,
+ FUN = function(set) {
+ set$simulationSet$outputs
+ }
)
- residualsHistogramPlot <- tlf::setPlotLabels(
- residualsHistogramPlot,
- ylabel = reEnv$residualsHistogramLabel
+ allOutputPaths <- sapply(
+ allOutputs,
+ FUN = function(output) {
+ output$path
+ }
)
+ allOutputs <- allOutputs[!duplicated(allOutputPaths)]
- residualsResults[[resultID]] <- saveTaskResults(
- id = resultID,
- plot = residualsHistogramPlot,
- plotCaption = captions$plotGoF$histogram(simulationSetNames, simulationSetDescriptor)
- )
+ selectedLogData <- data$Simulated > 0 & data$Observed > 0
- resultID <- defaultFileNames$resultID(
- "residuals-across-all-simulations-qq-plot"
- )
+ # Plot the residuals across the simulations by output path
+ for (output in allOutputs) {
+ Legend <- "Residuals\nlog(Observed)-log(Simulated)"
+ if (isIncluded(output$residualScale, ResidualScales$Logarithmic)) {
+ Legend <- "Residuals\nObserved-Simulated"
+ }
+ residualsMetaData <- list(
+ "Time" = list(dimension = "Time", unit = structureSets[[1]]$simulationSet$timeUnit),
+ "Observed" = list(dimension = "Observed data", unit = output$displayUnit),
+ "Simulated" = list(dimension = "Simulated value", unit = output$displayUnit),
+ "Residuals" = list(unit = "", dimension = Legend)
+ )
- residualsQQPlot <- tlf::plotQQ(
- data = data,
- metaData = metaData,
- dataMapping = tlf::QQDataMapping$new(
- y = "Residuals",
- group = "Legend"
- ),
- plotConfiguration = settings$plotConfigurations[["qqPlot"]]
- )
- residualsQQPlot <- tlf::setPlotLabels(
- residualsQQPlot,
- ylabel = reEnv$residualsQQLabel
- )
+ # Obs vs pred
+ obsVsPredPlot <- tlf::plotObsVsPred(
+ data = data[data$Path %in% output$path, ],
+ metaData = residualsMetaData,
+ dataMapping = tlf::ObsVsPredDataMapping$new(
+ x = "Observed",
+ y = "Simulated",
+ group = "Legend"
+ ),
+ plotConfiguration = settings$plotConfigurations[["obsVsPred"]]
+ )
- residualsResults[[resultID]] <- saveTaskResults(
- id = resultID,
- plot = residualsQQPlot,
- plotCaption = captions$plotGoF$qqPlot(simulationSetNames, simulationSetDescriptor)
- )
+ resultID <- defaultFileNames$resultID(
+ "residuals-across-all-simulations",
+ length(residualsResults),
+ "obsVsPred",
+ output$path
+ )
+ residualsResults[[resultID]] <- saveTaskResults(
+ id = resultID,
+ plot = obsVsPredPlot,
+ plotCaption = captions$plotGoF$obsVsPred(
+ simulationSetName = simulationSetNames,
+ descriptor = simulationSetDescriptor,
+ pathName = output$displayName
+ )
+ )
+
+ # Obs vs Pred log scale
+ if (sum(selectedLogData & data$Path %in% output$path) > 0) {
+ obsVsPredRange <- autoAxesLimits(c(
+ data$Simulated[selectedLogData & data$Path %in% output$path],
+ data$Observed[selectedLogData & data$Path %in% output$path]
+ ),
+ scale = "log"
+ )
+ obsVsPredBreaks <- autoAxesTicksFromLimits(obsVsPredRange)
+
+ obsVsPredPlotLog <- tlf::plotObsVsPred(
+ data = data[selectedLogData & data$Path %in% output$path, ],
+ metaData = residualsMetaData,
+ dataMapping = tlf::ObsVsPredDataMapping$new(
+ x = "Observed",
+ y = "Simulated",
+ group = "Legend"
+ ),
+ plotConfiguration = settings$plotConfigurations[["obsVsPred"]]
+ )
+ obsVsPredPlotLog <- tlf::setXAxis(
+ plotObject = obsVsPredPlotLog,
+ scale = tlf::Scaling$log,
+ limits = obsVsPredRange,
+ ticks = obsVsPredBreaks
+ )
+ obsVsPredPlotLog <- tlf::setYAxis(
+ plotObject = obsVsPredPlotLog,
+ scale = tlf::Scaling$log,
+ limits = obsVsPredRange,
+ ticks = obsVsPredBreaks
+ )
+
+ resultID <- defaultFileNames$resultID(
+ "residuals-across-all-simulations",
+ length(residualsResults),
+ "obsVsPredLog",
+ output$path
+ )
+ residualsResults[[resultID]] <- saveTaskResults(
+ id = resultID,
+ plot = obsVsPredPlotLog,
+ plotCaption = captions$plotGoF$obsVsPred(
+ simulationSetName = simulationSetNames,
+ descriptor = simulationSetDescriptor,
+ plotScale = "logarithmic",
+ pathName = output$displayName
+ )
+ )
+ }
+
+ # Res vs pred
+ resVsPredPlot <- tlf::plotResVsPred(
+ data = data[data$Path %in% output$path, ],
+ metaData = residualsMetaData,
+ dataMapping = tlf::ResVsPredDataMapping$new(
+ x = "Simulated",
+ y = "Residuals",
+ group = "Legend"
+ ),
+ plotConfiguration = settings$plotConfigurations[["resVsPred"]]
+ )
+
+ resultID <- defaultFileNames$resultID(
+ "residuals-across-all-simulations",
+ length(residualsResults),
+ "res-vs-pred"
+ )
+ residualsResults[[resultID]] <- saveTaskResults(
+ id = resultID,
+ plot = resVsPredPlot,
+ plotCaption = captions$plotGoF$resVsPred(
+ simulationSetName = simulationSetNames,
+ descriptor = simulationSetDescriptor,
+ plotScale = output$residualScale,
+ pathName = output$displayName
+ )
+ )
+
+ # Res vs time
+ residualTimeTicks <- getTimeTicksFromUnit(
+ residualsMetaData$Time$unit,
+ timeValues = data$Time
+ )
+ resVsTimePlot <- tlf::plotResVsTime(
+ data = data,
+ metaData = residualsMetaData,
+ dataMapping = tlf::ResVsTimeDataMapping$new(
+ x = "Time",
+ y = "Residuals",
+ group = "Legend"
+ ),
+ plotConfiguration = settings$plotConfigurations[["resVsTime"]]
+ )
+ resVsTimePlot <- tlf::setXAxis(
+ plotObject = resVsTimePlot,
+ ticks = residualTimeTicks$ticks,
+ ticklabels = residualTimeTicks$ticklabels
+ )
+
+ resultID <- defaultFileNames$resultID(
+ "residuals-across-all-simulations",
+ length(residualsResults),
+ "res-vs-time"
+ )
+ residualsResults[[resultID]] <- saveTaskResults(
+ id = resultID,
+ plot = resVsTimePlot,
+ plotCaption = captions$plotGoF$resVsTime(
+ simulationSetName = simulationSetNames,
+ descriptor = simulationSetDescriptor,
+ plotScale = output$residualScale,
+ pathName = output$displayName
+ )
+ )
+
+ # Histogram
+ residualsHistogramPlot <- tlf::plotHistogram(
+ data = data[data$Path %in% output$path, ],
+ metaData = residualsMetaData,
+ dataMapping = tlf::HistogramDataMapping$new(
+ x = "Residuals",
+ fill = "Legend",
+ stack = TRUE,
+ distribution = "normal"
+ ),
+ plotConfiguration = settings$plotConfigurations[["histogram"]],
+ bins = settings$bins %||% reEnv$defaultBins
+ )
+ residualsHistogramPlot <- tlf::setPlotLabels(
+ residualsHistogramPlot,
+ ylabel = reEnv$residualsHistogramLabel
+ )
+
+ resultID <- defaultFileNames$resultID(
+ "residuals-across-all-simulations",
+ length(residualsResults),
+ "histogram"
+ )
+ residualsResults[[resultID]] <- saveTaskResults(
+ id = resultID,
+ plot = residualsHistogramPlot,
+ plotCaption = captions$plotGoF$resHisto(
+ simulationSetName = simulationSetNames,
+ descriptor = simulationSetDescriptor,
+ plotScale = output$residualScale,
+ pathName = output$displayName
+ )
+ )
+
+ # QQ Plot
+ residualsQQPlot <- tlf::plotQQ(
+ data = data[data$Path %in% output$path, ],
+ metaData = residualsMetaData,
+ dataMapping = tlf::QQDataMapping$new(
+ y = "Residuals",
+ group = "Legend"
+ ),
+ plotConfiguration = settings$plotConfigurations[["qqPlot"]]
+ )
+ residualsQQPlot <- tlf::setPlotLabels(
+ residualsQQPlot,
+ ylabel = reEnv$residualsQQLabel
+ )
+
+ resultID <- defaultFileNames$resultID(
+ "residuals-across-all-simulations",
+ length(residualsResults),
+ "qq-plot"
+ )
+ residualsResults[[resultID]] <- saveTaskResults(
+ id = resultID,
+ plot = residualsQQPlot,
+ plotCaption = captions$plotGoF$resQQPlot(
+ simulationSetName = simulationSetNames,
+ descriptor = simulationSetDescriptor,
+ plotScale = output$residualScale,
+ pathName = output$displayName
+ )
+ )
+ }
return(residualsResults)
}
diff --git a/man/GofPlotTask.Rd b/man/GofPlotTask.Rd
index 3ac6ce89..05956913 100644
--- a/man/GofPlotTask.Rd
+++ b/man/GofPlotTask.Rd
@@ -118,7 +118,7 @@ Run task and save its output results
\subsection{Method \code{getResidualsResults()}}{
Get plot results for residuals across all simulations
\subsection{Usage}{
-\if{html}{\out{}}\preformatted{GofPlotTask$getResidualsResults(structureSets, data, metaData, settings)}\if{html}{\out{
}}
+\if{html}{\out{}}\preformatted{GofPlotTask$getResidualsResults(structureSets, data, settings)}\if{html}{\out{
}}
}
\subsection{Arguments}{
@@ -128,8 +128,6 @@ Get plot results for residuals across all simulations
\item{\code{data}}{data.frame}
-\item{\code{metaData}}{meta data on `data`}
-
\item{\code{settings}}{List of settings such as `PlotConfiguration` R6 class objects for each goodness of fit plot}
}
\if{html}{\out{}}