tests/dev/test-population-sensitivity-plot3.R

In Open-Systems-Pharmacology/OSPSuite.ReportingEngine: R package to create reports for the Open Systems Pharmacology models

rm(list = ls())
library(ospsuite)
graphics.off()
library(ospsuite.reportingengine)

simulationFile <- "./tests/data/input-data/RaltegravirSim.pkml"
populationFile1 <- "./tests/data/input-data/RalPop10.csv"
populationFile2 <- "./tests/data/input-data/LarPop10.csv"


ps1 <- PopulationSimulationSet$new(
  simulationSetName = "ral",
  simulationFile = simulationFile,
  populationFile = populationFile1,
  outputs = c(
    Output$new(path = "Organism|VenousBlood|Plasma|Raltegravir|Concentration", displayName = "op1"),
    Output$new(
      path = "Organism|ArterialBlood|Plasma|Raltegravir|Concentration", displayName = "op2",
      pkParameters = c(
        PkParameterInfo$new("t_max", "new_t_max"),
        PkParameterInfo$new("AUC_tEnd", "new_AUC_tEnd")
      )
    ),
    Output$new(
      path = "Organism|Lung|Interstitial|Raltegravir|Concentration", displayName = "op3",
      pkParameters = c(
        PkParameterInfo$new("C_max", "new_C_max"),
        PkParameterInfo$new("MRT", "new_MRT")
      )
    )
  )
)




ps2 <- PopulationSimulationSet$new(
  simulationSetName = "lar",
  simulationFile = simulationFile,
  populationFile = populationFile2,
  outputs = c(Output$new(
    path = "Organism|Lung|Interstitial|Raltegravir|Concentration", displayName = "op4",
    pkParameters = c(
      PkParameterInfo$new("C_max", "kai_C_max"),
      PkParameterInfo$new("MRT", "kai_MRT")
    )
  ))
)


pwf <- PopulationWorkflow$new(
  simulationSets = list(ps1, ps2),
  workflowFolder = "./tests/dev/popsens2",
  workflowType = PopulationWorkflowTypes$parallelComparison
)

pwf$simulate$settings$showProgress <- FALSE
pwf$simulate$inactivate()
pwf$calculatePKParameters$inactivate()
pwf$calculateSensitivity$inactivate()
pwf$plotSensitivity$inactivate()



pwf$calculateSensitivity$settings$showProgress <- TRUE
pwf$calculateSensitivity$settings$variableParameterPaths <- c(
  "Organism|Heart|Volume",
  "Organism|Lung|Volume",
  "Organism|Kidney|Volume",
  "Organism|Brain|Volume",
  "Organism|Muscle|Volume",
  "Organism|LargeIntestine|Volume",
  "Organism|PortalVein|Volume",
  "Organism|Spleen|Volume",
  "Organism|Skin|Volume",
  "Organism|Pancreas|Volume",
  "Organism|SmallIntestine|Mucosa|UpperIleum|Fraction mucosa",
  "Organism|SmallIntestine|Volume",
  "Organism|Lumen|Effective surface area variability factor",
  "Organism|Bone|Volume",
  "Organism|Stomach|Volume"
)

pwf$calculateSensitivity$settings$quantileVec <- c(0.25, 0.5, 0.75)

pwf$plotSensitivity$settings <- SensitivityPlotSettings$new(
  totalSensitivityThreshold = 0.9,
  maximalParametersPerSensitivityPlot = 12,
  xAxisFontSize = 10,
  yAxisFontSize = 6
)

pwf$runWorkflow()