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Carry out and visualize sensitivity analysis (with OSPSuite)

Source: R/sensitivity-calculation.R
sensitivityCalculation.Rd

Carry out and visualize sensitivity analysis (with OSPSuite)

Usage

sensitivityCalculation(
  simulation,
  outputPaths,
  parameterPaths,
  variationRange = c(seq(0.1, 1, by = 0.1), seq(2, 10, by = 1)),
  variationType = c("relative", "absolute"),
  pkParameters = c("C_max", "t_max", "AUC_inf"),
  customOutputFunctions = NULL,
  saOutputFilePath = NULL,
  simulationRunOptions = NULL
)

Arguments

simulation

An object of type Simulation.

outputPaths

Path (or a vector of paths) to the output(s) for which the sensitivity will be analyzed.

parameterPaths

A single or a vector of the parameter path(s) to be varied. Can also be a named vector, where the names are user-defined labels. These names will be stored and used in downstream plotting functions (e.g., as legend labels) if provided.

variationRange

Optional numeric vector or list defining the scaling of the parameters. The same variation range is applied to all specified parameters unless a list is provided, in which case the length of the list must match the length of parameterPaths, allowing individual variation for each parameter. If not specified, the following vector will be used: c(0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10).

variationType

A string specifying whether the values in variationRange are applied as "absolute" or "relative" scaling. When set to "absolute", the values are interpreted as absolute parameter values. When set to "relative", the values are interpreted as scaling factors relative to the initial parameter values. Default is "relative".

pkParameters

A vector of names of PK parameters for which the sensitivities will be calculated. For a full set of available standard PK parameters, run names(ospsuite::StandardPKParameter). By default, the following parameters are considered: "C_max", "t_max", "AUC_inf". If NULL, all available PK-parameters (including the user-defined) will be calculated.

customOutputFunctions

A named list with custom function(s) for output calculations. User-defined functions should have either 'x', 'y', or both 'x' and 'y' as parameters which correspond to x-Dimension (time) or y-Dimension values from simulation results. The output of the function is a single numerical value for each output and parameter path, which is then included in the returned dataframe of PK parameters.

saOutputFilePath

Path to excel file in which PK-parameter data should be saved. If a file already exists, it will be overwritten. Default is NULL, meaning the data will not be saved to a spreadsheet.

simulationRunOptions

Optional instance of a SimulationRunOptions used during the simulation run

Value

A list containing following objects:

  • SimulationResults

  • specified output paths

  • specified parameter paths

  • A data frame of PK parameters

See also

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

Examples

if (FALSE) { # \dontrun{
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"
)

# extract the results into a list of dataframes
sensitivityCalculation(
  simulation = simulation,
  outputPaths = outputPaths,
  parameterPaths = parameterPaths
)

# Calculate sensitivity for a user-defined function that computes the
# averate of the simulated y-values
customOutputFunctions <- list(
  "Average" = function(y) mean(y)
)
sensitivityCalculation(
  simulation = simulation,
  outputPaths = outputPaths,
  parameterPaths = parameterPaths,
  customOutputFunctions = customOutputFunctions
)
} # }