tests/testthat/test-plot-population-time-profile.R

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

# data to be used ---------------------------------------

# plotPopulationTimeProfile


# only simulated ------------------------

test_that("It respects custom plot configuration", {
  # Load simulation
  simFilePath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite")
  sim <- loadSimulation(simFilePath)

  populationResults <- importResultsFromCSV(
    simulation = sim,
    filePaths = system.file("extdata", "SimResults_pop.csv", package = "ospsuite")
  )

  myDataComb <- DataCombined$new()
  myDataComb$addSimulationResults(populationResults)

  myPlotConfiguration <- DefaultPlotConfiguration$new()
  myPlotConfiguration$title <- "My Plot Title"
  myPlotConfiguration$subtitle <- "My Plot Subtitle"
  myPlotConfiguration$caption <- "My Sources"

  set.seed(123)
  vdiffr::expect_doppelganger(
    title = "only sim",
    fig = plotPopulationTimeProfile(myDataComb, myPlotConfiguration)
  )
})

# both observed and simulated ------------------------

test_that("It produces expected plot for both observed and simulated datasets", {
  simFilePath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite")
  sim <- loadSimulation(simFilePath)

  outputPaths <- c(
    "Organism|PeripheralVenousBlood|Aciclovir|Plasma (Peripheral Venous Blood)",
    "Organism|Muscle|Intracellular|Aciclovir|Concentration"
  )

  simResults <- importResultsFromCSV(simulation = sim, filePaths = system.file("extdata", "SimResults_pop.csv", package = "ospsuite"))

  obsData <- lapply(
    c("ObsDataAciclovir_1.pkml", "ObsDataAciclovir_2.pkml", "ObsDataAciclovir_3.pkml"),
    function(x) loadDataSetFromPKML(system.file("extdata", x, package = "ospsuite"))
  )
  names(obsData) <- lapply(obsData, function(x) x$name)

  outputPaths <- "Organism|PeripheralVenousBlood|Aciclovir|Plasma (Peripheral Venous Blood)"
  myDataCombined <- DataCombined$new()

  # Add simulated results
  myDataCombined$addSimulationResults(
    simulationResults = simResults,
    quantitiesOrPaths = outputPaths,
    groups = "Aciclovir PVB"
  )

  # Add observed data set
  myDataCombined$addDataSets(obsData$`Vergin 1995.Iv`, groups = "Aciclovir PVB")

  myDataCombined$setDataTransformations(
    forNames = obsData$`Laskin 1982.Group D`$name,
    xOffsets = 2
  )

  myPlotConfiguration <- DefaultPlotConfiguration$new()
  myPlotConfiguration$yAxisScale <- "log"
  myPlotConfiguration$yAxisLimits <- c(0.01, 1000)

  set.seed(123)
  vdiffr::expect_doppelganger(
    title = "obs and sim",
    fig = plotPopulationTimeProfile(myDataCombined, myPlotConfiguration)
  )
})

# multiple datasets per group ---------------------

test_that("It produces expected plot for multple simulated datasets per group", {
  simFilePath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite")
  sim <- loadSimulation(simFilePath)

  outputPaths <- c(
    "Organism|PeripheralVenousBlood|Aciclovir|Plasma (Peripheral Venous Blood)",
    "Organism|Muscle|Intracellular|Aciclovir|Concentration"
  )

  simResults <- importResultsFromCSV(simulation = sim, filePaths = system.file("extdata", "SimResults_pop.csv", package = "ospsuite"))

  obsData <- lapply(
    c("ObsDataAciclovir_1.pkml", "ObsDataAciclovir_3.pkml"),
    function(x) loadDataSetFromPKML(system.file("extdata", x, package = "ospsuite"))
  )

  names(obsData) <- lapply(obsData, function(x) x$name)

  myDataCombined <- DataCombined$new()

  myDataCombined$addSimulationResults(
    simulationResults = simResults,
    quantitiesOrPaths = outputPaths,
    groups = "Aciclovir PVB"
  )

  set.seed(123)
  vdiffr::expect_doppelganger(
    title = "multiple sim",
    fig = plotPopulationTimeProfile(myDataCombined)
  )
})

test_that("It produces expected plot for multple simulated and observed datasets per group", {
  simFilePath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite")
  sim <- loadSimulation(simFilePath)

  outputPaths <- c(
    "Organism|PeripheralVenousBlood|Aciclovir|Plasma (Peripheral Venous Blood)",
    "Organism|Muscle|Intracellular|Aciclovir|Concentration"
  )

  simResults <- importResultsFromCSV(simulation = sim, filePaths = system.file("extdata", "SimResults_pop.csv", package = "ospsuite"))

  obsData <- lapply(
    c("ObsDataAciclovir_1.pkml", "ObsDataAciclovir_3.pkml"),
    function(x) loadDataSetFromPKML(system.file("extdata", x, package = "ospsuite"))
  )

  names(obsData) <- lapply(obsData, function(x) x$name)

  myDataCombined <- DataCombined$new()

  myDataCombined$addSimulationResults(
    simulationResults = simResults,
    quantitiesOrPaths = outputPaths,
    groups = "Aciclovir PVB"
  )

  myDataCombined$addDataSets(obsData, groups = "Aciclovir observed")

  set.seed(123)
  vdiffr::expect_doppelganger(
    title = "multiple sim and obs",
    fig = plotPopulationTimeProfile(myDataCombined)
  )
})

# edge cases ------------------------

test_that("It returns `NULL` when `DataCombined` is empty", {
  myCombDat <- DataCombined$new()

  expect_null(suppressWarnings(plotPopulationTimeProfile(myCombDat)))
  expect_warning(
    plotPopulationTimeProfile(myCombDat),
    messages$plottingWithEmptyDataCombined()
  )
})

# Aggregations ------------------------

test_that("Aggregations are computed and displayed correctly", {
  # Load simulation
  simFilePath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite")
  sim <- loadSimulation(simFilePath)

  populationResults <- importResultsFromCSV(
    simulation = sim,
    filePaths = system.file("extdata", "SimResults_pop.csv", package = "ospsuite")
  )

  myDataComb <- DataCombined$new()
  myDataComb$addSimulationResults(populationResults)

  vdiffr::expect_doppelganger(
    title = "default (quantiles)",
    fig = plotPopulationTimeProfile(myDataComb)
  )

  vdiffr::expect_doppelganger(
    title = "modified quantiles",
    fig = plotPopulationTimeProfile(myDataComb,
      quantiles = c(0.1, 0.5, 0.9)
    )
  )

  vdiffr::expect_doppelganger(
    title = "arithmetic mean",
    fig =
      plotPopulationTimeProfile(myDataComb,
        aggregation = "arithmetic"
      )
  )

  vdiffr::expect_doppelganger(
    title = "arithmetic mean with 2sd",
    fig =
      plotPopulationTimeProfile(myDataComb,
        aggregation = "arithmetic",
        nsd = 2
      )
  )


  vdiffr::expect_doppelganger(
    title = "geometric mean",
    fig = plotPopulationTimeProfile(myDataComb,
      aggregation = "geometric"
    )
  )

  vdiffr::expect_doppelganger(
    title = "geometric mean with 2sd",
    fig = plotPopulationTimeProfile(myDataComb,
      aggregation = "geometric",
      nsd = 2
    )
  )
})