tests/dev/script-pk-analyses.R

In Open-Systems-Pharmacology/OSPSuite-R: R package to manipulate OSPSuite Models

library(ospsuite)

# Remove to ensure that we can add the parameters again
removeAllUserDefinedPKParameters()

pkParameter <- updatePKParameter(name = "t_max", displayName = "MyTmax", displayUnit = "min")
print(pkParameter)

pkParameter <- updatePKParameter(name = "C_max", displayName = "MyCMax", displayUnit = "mg/ml")
print(pkParameter)

userDefinedPKParameter <- addUserDefinedPKParameter(name = "Test", standardPKParameter = StandardPKParameter$AUC_tEnd, displayName = "toto", displayUnit = "mg")
userDefinedPKParameter$normalizationFactor <- 100

quantityPath <- "Organism|PeripheralVenousBlood|Caffeine|Plasma (Peripheral Venous Blood)"

sim <- loadSimulation("tests/data/S1.pkml")
toto <- sim$molWeightFor(quantityPath)

popFile <- getTestDataFilePath("pop.csv")
population <- loadPopulation(popFile)
simRunOptions <- SimulationRunOptions$new(numberOfCores = 4, checkForNegativeValues = TRUE, showProgress = TRUE)
populationResults <- runSimulations(sim, population, simRunOptions)[[1]]
populationPkAnalyses <- calculatePKAnalyses(populationResults)
df <- pkAnalysesToDataFrame(populationPkAnalyses)

exportPKAnalysesToCSV(populationPkAnalyses, "C:/temp/export/pk.csv")
newPKAnalyses <- importPKAnalysesFromCSV("C:/temp/export/pk.csv", sim)
df <- pkAnalysesToDataFrame(newPKAnalyses)

print(populationPkAnalyses)
pkParameters <- populationPkAnalyses$allPKParametersFor(quantityPath)

for (pkParameter in pkParameters) {
  print(pkParameter)
}

allPKParameterNames()