sensitivityTimeProfiles: Time Profile plots for Sensitivity Analysis

In esqLABS/esqlabsR: esqLABS utilities package

Time Profile plots for Sensitivity Analysis

Description

Creates time profiles for selected outputs generated in a sensitivity analysis. This function plots time profiles for each specified output path, illustrating the dynamics of model outputs to parameter variations.

Usage

sensitivityTimeProfiles(
  sensitivityCalculation,
  outputPaths = NULL,
  parameterPaths = NULL,
  xAxisScale = NULL,
  yAxisScale = NULL,
  xUnits = NULL,
  yUnits = NULL,
  observedData = NULL,
  defaultPlotConfiguration = NULL
)

Arguments

sensitivityCalculation	The SensitivityCalculation object returned by sensitivityCalculation().
outputPaths, parameterPaths	A single or a vector of the output path(s) to be plotted for parameter path(s) which impact is analyzed, respectively. If NULL, all included paths and parameters present in the supplied SensitivityCalculation object will be displayed in the visualization. A separate plot will be generated for each output path, and a separate curve will be generated for each parameter variation. A separate panel is created for each varied parameter.
xAxisScale	Character string, either "log" (logarithmic scale) or "lin" (linear scale), to set the x-axis scale. Default is "lin".
yAxisScale	Character string, either "log" or "lin", sets the y-axis scale similarly to xAxisScale. Default is "log".
xUnits, yUnits	Lists of units for the x-axis and y-axis, respectively. If a list of length one is provided, it will be applied to all outputPaths if conversion is possible. If a list of multiple units is provided, the units list should correspond to the outputPaths, and units conversion will be applied accordingly. If NULL, default units from the simulation results will be used.
observedData	Optional. A set of DataSet objects containing observed data. If provided, observed data will be plotted together with the simulated data based on OutputPath dimension for direct comparison within the visualizations. Will be added only to plots with matching y dimension.
defaultPlotConfiguration	An object of class DefaultPlotConfiguration used to customize plot aesthetics. Plot-specific settings provided directly to the function, such as xAxisScale, will take precedence over any modifications in defaultPlotConfiguration. If not provided, default settings are applied. Supported parameters for defaultPlotConfiguration include: legendPosition: Specifies the position of the plot legend. legendTitle: Sets the title displayed for the legend. linesAlpha: Alpha transparency for the line elements. linesColor: Color of the line elements. linesSize: Thickness of the line elements. pointsShape: Shape of the point elements for observed data. title: Main title text for the plot. titleSize: Font size of the plot title. xAxisScale: Scale type for the x-axis ("log" or "lin"). xLabel: Label text for the x-axis. yAxisScale: Scale type for the y-axis ("log" or "lin"). yLabel: Label text for the y-axis.

Value

A patchwork object containing the combined ggplot objects if a single output path is specified, or a list of patchwork objects for multiple output paths.

See Also

Other sensitivity-calculation: sensitivityCalculation(), sensitivitySpiderPlot(), sensitivityTornadoPlot()

Examples

## Not run: 
simPath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite")
simulation <- loadSimulation(simPath)
outputPaths <- "Organism|PeripheralVenousBlood|Aciclovir|Plasma (Peripheral Venous Blood)"
parameterPaths <- c(
  "Aciclovir|Lipophilicity",
  "Applications|IV 250mg 10min|Application_1|ProtocolSchemaItem|Dose",
  "Neighborhoods|Kidney_pls_Kidney_ur|Aciclovir|Glomerular Filtration-GFR|GFR fraction"
)

results <- sensitivityCalculation(
  simulation = simulation,
  outputPaths = outputPaths,
  parameterPaths = parameterPaths
)

# Print plots with default settings
sensitivityTimeProfiles(results)

# Print plots with linear y-axis values
sensitivityTimeProfiles(results, yAxisScale = "lin")

# Print plots with custom configuration settings
myPlotConfiguration <- createEsqlabsPlotConfiguration()
myPlotConfiguration$linesColor <- c("#4D8076", "#C34A36")
myPlotConfiguration$subtitle <- "Custom settings"
sensitivityTimeProfiles(results, defaultPlotConfiguration = myPlotConfiguration)

# Use named parameter paths to customize facet labels
namedParameterPaths <- c(
  "Lipophilicity" = "Aciclovir|Lipophilicity",
  "Dose" = "Applications|IV 250mg 10min|Application_1|ProtocolSchemaItem|Dose",
  "GFR fraction" = "Neighborhoods|Kidney_pls_Kidney_ur|Aciclovir|Glomerular Filtration-GFR|GFR fraction"
)

resultsNamed <- sensitivityCalculation(
  simulation = simulation,
  outputPaths = outputPaths,
  parameterPaths = namedParameterPaths
)

sensitivitySpiderPlot(resultsNamed)

## End(Not run)

esqLABS/esqlabsR documentation built on April 17, 2025, 10:51 a.m.