tests/testthat/test-simulate_scenarios.R

In campsis: Generic PK/PD Simulation Platform Campsis

library(testthat)

context("Test the simulate method with scenarios")

seed <- 1
source(file.path(getwd(), test_path(), "test-utils.R"))

test_that("Simulate scenarios - make few changes on dataset", {
  model <- model_suite$testing$nonmem$advan4_trans4
  regFilename <- "scenarios_few_changes_on_dataset"

  dataset <- Dataset() %>%
    add(Observations(times = seq(0, 24, by = 3)))

  scenarios <- Scenarios() %>%
    add(Scenario("1000 mg SD", dataset = ~ .x %>% set_subjects(2) %>% add(Bolus(time = 0, 1000)))) %>%
    add(Scenario("1500 mg SD", dataset = ~ .x %>% set_subjects(2) %>% add(Bolus(time = 0, 1500)))) %>%
    add(Scenario("2000 mg SD", dataset = ~ .x %>% set_subjects(4) %>% add(Bolus(time = 0, 2000))))

  simulation <- expression(simulate(
    model = model,
    dataset = dataset,
    dest = destEngine,
    scenarios = scenarios,
    seed = seed,
    outvars = "KA"
  ))
  test <- expression(
    spaghettiPlot(results, "CP", "SCENARIO") + ggplot2::facet_wrap(~SCENARIO),
    output_regression_test(results, output = c("SCENARIO", "CP"), filename = regFilename),
    expect_equal(results$SCENARIO %>% unique(), c("1000 mg SD", "1500 mg SD", "2000 mg SD")),

    # Check some 'properties' of the scenarios:
    results$EPS_PROP <- (results$OBS_CP / results$CP) - 1,
    res_scenario1 <- results %>% dplyr::filter(SCENARIO == "1000 mg SD"),
    res_scenario2 <- results %>% dplyr::filter(SCENARIO == "1500 mg SD"),
    res_scenario3 <- results %>% dplyr::filter(SCENARIO == "2000 mg SD"),

    # 1) ID's start at 1 in each scenario
    expect_equal(res_scenario1$ID %>% unique(), c(1, 2)),
    expect_equal(res_scenario2$ID %>% unique(), c(1, 2)),
    expect_equal(res_scenario3$ID %>% unique(), c(1, 2, 3, 4)),

    # 2) Same seed is used in each scenario -> same ETA's if same number of subjects
    expect_equal(res_scenario1$KA %>% unique(), res_scenario2$KA %>% unique()),

    # 3) Same seed is used in each scenario -> same residual variability if same number of subjects & same protocol
    expect_equal(res_scenario1$EPS_PROP, res_scenario2$EPS_PROP)
  )
  campsis_test(simulation, test, env = environment())
})

test_that("Simulate scenarios - make few changes on model", {
  model <- model_suite$testing$nonmem$advan4_trans4
  regFilename <- "scenarios_few_changes_on_model"

  dataset <- Dataset(3) %>%
    add(Bolus(time = 0, amount = 1000)) %>%
    add(Observations(times = c(0, 1, 2, 3, 4, 5, 6, 12, 24)))

  scenarios <- Scenarios() %>%
    add(Scenario("THETA_KA=1", model = ~ .x %>% replace(Theta(name = "KA", value = 1)))) %>%
    add(Scenario("THETA_KA=3", model = ~ .x %>% replace(Theta(name = "KA", value = 3)))) %>%
    add(Scenario("THETA_KA=6") %>% add(ReplaceAction(Theta(name = "KA", value = 6))))

  # Running scenarios sequentially with only 1 CPU
  setup_plan_sequential()
  settings <- Settings()

  simulation <- expression(simulate(
    model = model,
    dataset = dataset,
    dest = destEngine,
    scenarios = scenarios,
    seed = seed,
    settings = settings
  ))
  test <- expression(
    spaghettiPlot(results, "CP", "SCENARIO") + ggplot2::facet_wrap(~SCENARIO),
    output_regression_test(results, output = c("SCENARIO", "CP"), filename = regFilename)
  )
  campsis_test(simulation, test, env = environment())

  # Running scenarios in parallel with 3 CPU's
  settings <- Settings(Hardware(cpu = 3, scenario_parallel = TRUE))

  simulation <- expression(simulate(
    model = model,
    dataset = dataset,
    dest = destEngine,
    scenarios = scenarios,
    seed = seed,
    settings = settings
  ))
  test <- expression(
    spaghettiPlot(results, "CP", "SCENARIO") + ggplot2::facet_wrap(~SCENARIO),
    output_regression_test(results, output = c("SCENARIO", "CP"), filename = regFilename)
  )
  campsis_test(simulation, test, env = environment())

  # Back to sequential
  setup_plan_sequential()
})

test_that("Export 'SCENARIO' column as soon as 1 scenario is specified.", {
  model <- model_suite$testing$nonmem$advan4_trans4

  dataset <- Dataset(3) %>%
    add(Bolus(time = 0, amount = 1000)) %>%
    add(Observations(times = c(0, 1, 2, 3, 4, 5, 6, 12, 24)))

  # Scenarios are NULL
  scenarios <- NULL

  simulation <- expression(simulate(
    model = model,
    dataset = dataset,
    dest = destEngine,
    scenarios = scenarios,
    seed = seed
  ))
  test <- expression(
    expect_equal(nrow(results), 3 * 9),
    expect_false("SCENARIO" %in% colnames(results))
  )
  campsis_test(simulation, test, env = environment())

  # Scenarios are empty
  scenarios <- Scenarios()

  simulation <- expression(simulate(
    model = model,
    dataset = dataset,
    dest = destEngine,
    scenarios = scenarios,
    seed = seed
  ))
  test <- expression(
    expect_equal(nrow(results), 3 * 9),
    expect_false("SCENARIO" %in% colnames(results))
  )
  campsis_test(simulation, test, env = environment())

  # 1 scenario is provided
  scenarios <- Scenarios() %>%
    add(Scenario(name = "My scenario"))

  simulation <- expression(simulate(
    model = model,
    dataset = dataset,
    dest = destEngine,
    scenarios = scenarios,
    seed = seed
  ))
  test <- expression(
    expect_equal(nrow(results), 3 * 9),
    expect_true("SCENARIO" %in% colnames(results)),
    expect_true(results$SCENARIO %>% unique() == "My scenario")
  )
  campsis_test(simulation, test, env = environment())
})