tests/testthat/test-json_interface.R

In campsis: Generic PK/PD Simulation Platform Campsis

library(testthat)

context("Test the JSON interface")

testFolder <- file.path(getwd(), test_path())

test_that("Import a few basic Campsis datasets from JSON", {
  # 1A
  dataset1a <- Dataset(json = file.path(testFolder, "json_examples", "dataset_example1a.json"))

  expArm1 <- Arm(subjects = 100, label = "Arm 1") %>%
    add(Bolus(time = 0, amount = 50, compartment = "ABS", ii = 24, addl = 6)) %>%
    add(Infusion(time = 0, amount = 50, compartment = "CENTRAL", ii = 24, addl = 6, duration = 2))
  expArm2 <- Arm(subjects = 100, label = "Arm 2") %>%
    add(Bolus(time = 0, amount = 100, compartment = "ABS", ii = 24, addl = 6))
  expDataset1a <- Dataset() %>%
    add(expArm1) %>%
    add(expArm2) %>%
    add(Observations(seq(0, 168, by = 24)))

  expect_equal(dataset1a, expDataset1a)

  # 1B
  dataset1b <- Dataset(json = file.path(testFolder, "json_examples", "dataset_example1b.json"))
  expDataset1b <- Dataset() %>%
    add(expArm1) %>%
    add(expArm2) %>%
    add(Observations(TimeSequence(0, 168, by = 1)))

  expect_equal(dataset1b, expDataset1b)

  # 1C
  dataset1c <- Dataset(json = file.path(testFolder, "json_examples", "dataset_example1c.json"))
  expDataset1c <- Dataset() %>%
    add(expArm1) %>%
    add(expArm2) %>%
    add(Observations(TimeSequence(0, 24, by = 1), rep = DosingSchedule()))

  expect_equal(dataset1c, expDataset1c)

  # 1D = 1A but all time units in days
  dataset1d <- Dataset(json = file.path(testFolder, "json_examples", "dataset_example1d.json"))
  expect_equal(dataset1d, expDataset1a)

  # 1E = 1B but all time units in days
  dataset1e <- Dataset(json = file.path(testFolder, "json_examples", "dataset_example1e.json"))
  expect_equal(dataset1e, expDataset1b)

  # Example 2: dataset settings
  dataset2 <- Dataset(json = file.path(testFolder, "json_examples", "dataset_example2.json"))
  expArm2 <- Arm(subjects = 100, label = "My dataset") %>%
    add(Bolus(time = 0, amount = 100, compartment = "ABS", ii = 24, addl = 6)) %>%
    add(Observations(TimeSequence(0, 24, by = 1), rep = DosingSchedule()))
  expDataset2 <- Dataset() %>%
    add(expArm2) %>%
    add(DatasetConfig(exportTSLD = TRUE, exportTDOS = TRUE, timeUnitExport = "day"))

  expect_equal(dataset2, expDataset2)

  # Example 3: dataset covariates
  dataset3 <- Dataset(json = file.path(testFolder, "json_examples", "dataset_example3_covariates.json"))
  expArm3 <- Arm(subjects = 100, label = "My dataset") %>%
    add(Observations(TimeSequence(0, 24, by = 1))) %>%
    add(Covariate("BW1", 70.5)) %>%
    add(Covariate("BW2", c(70.5, 80.5, 90.5))) %>%
    add(Covariate("BW3", NormalDistribution(70.5, 10.5))) %>%
    add(Covariate("BW4", UniformDistribution(50.0, 100.0))) %>%
    add(Covariate("BW5", LogNormalDistribution(4.5, 2.3))) %>%
    add(Covariate("SEX", DiscreteDistribution(x = c(0, 1), c(0.6, 0.4))))
  expDataset3 <- Dataset() %>%
    add(expArm3)

  expect_equal(dataset3, expDataset3)
})

test_that("Import Campsis datasets that include a dose adaptation layer from JSON", {
  dataset <- Dataset(json = file.path(testFolder, "json_examples", "dataset_dose_adaptation_example1.json"))
  expArm <- Arm(subjects = 100, label = "My dataset") %>%
    add(Bolus(time = 0, amount = 50, compartment = "ABS", ii = 24, addl = 0)) %>%
    add(Observations(TimeSequence(0, 24, by = 1))) %>%
    add(Covariate("BW", NormalDistribution(70.5, 10.5))) %>%
    add(DoseAdaptation("AMT*WT", compartments = "ABS")) %>%
    add(DoseAdaptation("TO_ALL_CMTS"))
  expDataset <- Dataset() %>%
    add(expArm)

  expect_equal(dataset, expDataset)
})

test_that("Import Campsis datasets that include a bootstrap layer from JSON", {
  # Example 1 with bootstrap
  dataset1 <- Dataset(json = file.path(testFolder, "json_examples", "dataset_bootstrap_example1.json"))

  expArm1 <- Arm(subjects = 100, label = "My dataset") %>%
    add(Observations(TimeSequence(0, 24, by = 1))) %>%
    add(Bootstrap(
      data = data.frame(BS_ID = c(1, 2, 3), BW = c(70, 75, 80), AGE = c(30, 35, 40)),
      replacement = TRUE,
      random = TRUE,
      export_id = TRUE
    ))

  expDataset1 <- Dataset() %>%
    add(expArm1)

  expect_equal(dataset1, expDataset1)

  # Example 2 with bootstrap (same but no row identifier)
  dataset2 <- Dataset(json = file.path(testFolder, "json_examples", "dataset_bootstrap_example2.json"))
  expect_equal(dataset2, expDataset1)
  expect_equal(dataset1, dataset2)
})

test_that("Import Campsis datasets that include a cyclic treatment schedule from JSON", {
  dataset1 <- Dataset(json = file.path(testFolder, "json_examples", "dataset_cyclic_schedule_example1.json"))

  expArm1 <- Arm(subjects = 100, label = "My dataset") %>%
    add(Bolus(
      time = 0,
      amount = 50,
      compartment = "ABS",
      ii = 24,
      addl = 6,
      rep = CyclicSchedule(duration = 24 * 28, repetitions = 1)
    )) %>%
    add(Observations(TimeSequence(0, 24, by = 1), rep = DosingSchedule()))

  expDataset1 <- Dataset() %>%
    add(expArm1)

  expect_equal(dataset1, expDataset1)

  # Same but duration in hours and unit is not specified
  dataset2 <- Dataset(json = file.path(testFolder, "json_examples", "dataset_cyclic_schedule_example2.json"))
  expect_equal(dataset2, expDataset1)
})

test_that("Import Campsis settings in JSON format", {
  # 1A
  settings1a <- Settings(json = file.path(testFolder, "json_examples", "settings_example1a.json"))
  expSettings1a <- Settings(DefaultSettings(
    engine = "mrgsolve",
    seed = 1,
    outvars = c("CONC", "CONC_ERR"),
    disabled_variabilities = "IIV"
  ))

  expect_equal(settings1a, expSettings1a)

  # 1B
  settings1b <- Settings(json = file.path(testFolder, "json_examples", "settings_example1b.json"))
  expSettings1b <- Settings(DefaultSettings(engine = "mrgsolve", seed = 1, outvars = c("CONC", "CONC_ERR")))

  expect_equal(settings1b, expSettings1b)

  # CTS settings (example 1)
  settings_cts1 <- Settings(json = file.path(testFolder, "json_examples", "settings_cts_example1.json"))
  exp_outfuns_cts1 <- Outfuns() %>%
    add(DefaultOutfun()) %>%
    add(PIOutfun(variable = "CONC", name = "PI 90%", level = 0.9)) %>%
    add(StatsOutfun(variable = "CONC", name = "Statistics on CONC", stats = c("median", "p5", "p95")))
  exp_settings_cts1 <- Settings(DefaultSettings(
    engine = "mrgsolve",
    seed = 1,
    outvars = c("CONC", "CONC_ERR"),
    outfuns = exp_outfuns_cts1
  ))
  expect_equal(settings_cts1, exp_settings_cts1)
})

test_that("Import Campsis settings that include a NCA table outfun from JSON", {
  if (skip_long_tests()) {
    # Long tests are not executed on CRAN
    # Here I don't to create a dependency to campsisnca in the Campsis tests
    return(TRUE)
  }
  skip_if_not_installed("campsisnca")
  library(campsisnca)

  settings_cts3 <- Settings(json = file.path(testFolder, "json_examples", "settings_cts_example3.json"))

  # NCA table, as passed to the 'table' property of a 'nca_table_outfun' (JSON-encoded string)
  nca_table_json <- paste0(
    '{"nca_analyses":[{"name":"Default","variable":"CONC",',
    '"window":{"start":0,"end":"last"},',
    '"metrics":[{"type":"auc_metric","name":"AUC"}]}]}'
  )

  exp_outfun_cts3 <- NCATableOutfun(name = "nca_default", table = nca_table_json, export_type = "summary")
  exp_settings_cts3 <- Settings(DefaultSettings(
    engine = "mrgsolve",
    seed = 1,
    outvars = "CONC",
    outfuns = Outfuns() %>% add(exp_outfun_cts3)
  ))

  expect_equal(settings_cts3, exp_settings_cts3)
})

test_that("Import Campsis settings with replicates from JSON", {
  # replicates field present → loaded and stored correctly
  settings_rep <- Settings(json = file.path(testFolder, "json_examples", "settings_example_replicates.json"))
  exp_settings_rep <- Settings(DefaultSettings(engine = "rxode2", seed = 42, replicates = 100L))
  expect_equal(settings_rep, exp_settings_rep)

  # replicates field absent → defaults to 1L
  settings_no_rep <- Settings(json = file.path(testFolder, "json_examples", "settings_example1b.json"))
  expect_equal(settings_no_rep@default@replicates, 1L)

  # replicates field present + hardware settings
  settings_rep <- Settings(json = file.path(testFolder, "json_examples", "settings_example_replicates_hardware.json"))
  exp_settings_rep <- Settings(
    DefaultSettings(engine = "rxode2", seed = 42, replicates = 100L),
    Hardware(cpu = 4, replicate_parallel = TRUE)
  )
  expect_equal(settings_rep, exp_settings_rep)
})

test_that("Import Campsis scenarios in JSON format", {
  # 1A
  scenarios1a <- Scenarios(json = file.path(testFolder, "json_examples", "scenarios_example1a.json"))

  expScenarios1a <- Scenarios() %>%
    add(Scenario(name = "Base scenario")) %>%
    add(
      Scenario(name = "Slow KA") %>%
        add(ReplaceAction(Theta(name = "KA", value = 0.3, label = "Absorption rate", unit = "1/h")))
    )

  expect_equal(scenarios1a, expScenarios1a)

  expect_true("Scenario 'Base scenario'" %in% capture.output(show(scenarios1a)))
  expect_true("Scenario 'Slow KA'" %in% capture.output(show(scenarios1a)))
})