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runSU

Source: R/su-functions.R
runSU.Rd

Function to run sensitivity analysis and then run uncertainy analysis for parameters deemed sensitive. Main parameters:

Usage

runSU(
  simulation,
  DDIsimulation = NULL,
  customParameters = NULL,
  outputs,
  evaluateForAllParameters = FALSE,
  variationRange = 0.1,
  numberOfSensitivityAnalysisSteps = 2,
  sensitivityThreshold = 0.1,
  runUncertaintyAnalysis = TRUE,
  runUncertaintlyOnlyForSensitiveParameters = TRUE,
  numberOfUncertaintyAnalysisSamples = 100,
  quantiles = c(0.05, 0.5, 0.95),
  saveResults = FALSE,
  saveFolder = NULL,
  saveFileName = NULL,
  runParallel = TRUE,
  updateProgressSensitivity = NULL,
  updateProgressUncertainty = NULL
)

Arguments

simulation

PKML simulation object.

DDIsimulation

DDI PKML simulation object.

customParameters

List of SAParameter objects with user-specified distributions.

outputs

List of SAOutput objects.

evaluateForAllParameters

Logical value. If TRUE, all model parameters will be evaluated for sensitivity and those with a sensitivity greater than sensitivityThreshold will undergo uncertainty analysis. Any parameters not included in the customParameters list will have a log-uniform distribution with bounds set by variationRange. Sensitivity analysis settings:

variationRange

The variation range used to define the log-uniform distribution of the parameters in parameterPaths.

numberOfSensitivityAnalysisSteps

Positive integer. Number of steps at which the model is simulated within a parameter's variationRange during the sensitivity analysis.

sensitivityThreshold

Positive numeric value. The threshold sensitivity above which a parameter will undergo uncertainty analysis if runUncertaintyAnalysis and runUncertaintlyOnlyForSensitiveParameters are both TRUE. Uncertainty analysis settings:

runUncertaintyAnalysis

Logical value. If TRUE, uncertainty analysis will run.

runUncertaintlyOnlyForSensitiveParameters

Logical value. If TRUE, uncertainty analysis will only be run for the parameters for which sensitivity exceeds sensitivityThreshold.

numberOfUncertaintyAnalysisSamples

Positive integer value giving the number of Monte Carlo runs for each parameter.

quantiles

Vector of numerical values between 0 and 1. The quantiles input sets the percentiles of the PK parameters to be evaluated in addition to the 50% and 95% percentiles, which are computed by default. Save settings:

saveResults

Logical value. If TRUE, the results will be saved.

saveFolder

String indicating the path to the folder in which the results are to be saved.

saveFileName

String indicating the file name to use when saving the results. Parallel run and updating settings

runParallel

Logical value. Sensitivity computation is run in parallel when TRUE.

updateProgressSensitivity

Logical value. Updates shiny app GUI with sensitivity analysis progress when TRUE.

updateProgressUncertainty

Logical value. Updates shiny app GUI with uncertainty analysis progress when TRUE.

Value

Sensitivity and uncertainty analysis results.