tests/testthat/test-simulate_infusion.R

In campsis: Generic PK/PD Simulation Platform Campsis

library(testthat)

context("Test the simulate method with infusions")

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

test_that("Simulate infusion using duration in dataset, then in model", {
  if (skip_long_tests()) {
    return(TRUE)
  }
  model <- model_suite$testing$nonmem$advan3_trans4
  regFilename <- "infusion_duration"

  # 5 hours infusion duration implemented in dataset
  dataset <- Dataset() %>%
    add(Infusion(time = 0, amount = 1000, compartment = 1, duration = 5)) %>%
    add(Observations(times = seq(0, 24, by = 0.5)))

  dataset_regression_test(dataset, model, seed = seed, filename = regFilename)

  simulation <- expression(simulate(model = model, dataset = dataset, dest = destEngine, seed = seed))
  test <- expression(
    expect_equal(nrow(results), 49),
    output_regression_test(results, output = "CP", filename = regFilename)
  )
  campsis_test(simulation, test, env = environment())

  # 5 hours infusion duration implemented in model
  dataset <- Dataset() %>%
    add(Infusion(time = 0, amount = 1000, compartment = 1)) %>%
    add(Observations(times = seq(0, 24, by = 0.5)))

  model <- model %>% add(InfusionDuration(compartment = 1, rhs = "5"))

  simulation <- expression(simulate(model = model, dataset = dataset, dest = destEngine, seed = seed))
  test <- expression(
    expect_equal(nrow(results), 49),
    output_regression_test(results, output = "CP", filename = regFilename)
  )
  campsis_test(simulation, test, env = environment())
})

test_that("Simulate infusion using rate in dataset", {
  model <- model_suite$testing$nonmem$advan3_trans4
  regFilename <- "infusion_duration"

  # 5 hours infusion duration implemented in dataset
  dataset <- Dataset() %>%
    add(Infusion(time = 0, amount = 1000, compartment = 1, rate = 200)) %>%
    add(Observations(times = seq(0, 24, by = 0.5)))

  dataset_regression_test(dataset, model, seed = seed, filename = regFilename)

  simulation <- expression(simulate(model = model, dataset = dataset, dest = destEngine, seed = seed))
  test <- expression(
    expect_equal(nrow(results), 49),
    output_regression_test(results, output = "CP", filename = regFilename)
  )
  campsis_test(simulation, test, env = environment())

  # 5 hours infusion duration implemented in model
  dataset <- Dataset()
  dataset <- dataset %>% add(Infusion(time = 0, amount = 1000, compartment = 1))
  dataset <- dataset %>% add(Observations(times = seq(0, 24, by = 0.5)))

  model <- model %>% add(InfusionRate(compartment = 1, rhs = "200"))

  simulation <- expression(simulate(model = model, dataset = dataset, dest = destEngine, seed = seed))
  test <- expression(
    expect_equal(nrow(results), 49),
    output_regression_test(results, output = "CP", filename = regFilename)
  )
  campsis_test(simulation, test, env = environment())
})

test_that("Simulate infusion using rate and lag time in dataset", {
  model <- model_suite$testing$nonmem$advan3_trans4
  regFilename <- "infusion_rate_lag_time1_dataset"

  # 5 hours duration
  duration <- 5
  # 2 hours lag time with 20% CV
  lag <- FunctionDistribution(fun = "rlnorm", args = list(meanlog = log(2), sdlog = 0.2))

  dataset <- Dataset(10) %>%
    add(Infusion(time = 0, amount = 1000, compartment = 1, duration = duration, lag = lag)) %>%
    add(Observations(times = seq(0, 24, by = 0.5)))

  dataset_regression_test(dataset, model, seed = seed, filename = regFilename)

  simulation <- expression(simulate(model = model, dataset = dataset, dest = destEngine, seed = seed))
  test <- expression(
    expect_equal(nrow(results), 49 * dataset %>% length()),
    output_regression_test(results, output = "CP", filename = regFilename)
  )
  campsis_test(simulation, test, env = environment())
})

test_that("Simulate infusion using rate and lag time (parameter distribution) in dataset", {
  model <- model_suite$testing$nonmem$advan3_trans4
  regFilename <- "infusion_rate_lag_time2_dataset"
  model <- model %>% add(Theta(name = "ALAG1", index = 5, value = 2)) # 2 hours lag time
  model <- model %>% add(Omega(name = "ALAG1", index = 5, index2 = 5, value = 0.2^2)) #20% CV

  dataset <- Dataset(10)
  lag <- ParameterDistribution(model, theta = "ALAG1", omega = "ALAG1")
  dataset <- dataset %>% add(Infusion(time = 0, amount = 1000, compartment = 1, rate = 200, lag = lag))
  dataset <- dataset %>% add(Observations(times = seq(0, 24, by = 0.5)))

  dataset_regression_test(dataset, model, seed = seed, filename = regFilename)

  simulation <- expression(simulate(model = model, dataset = dataset, dest = destEngine, seed = seed))
  test <- expression(
    expect_equal(nrow(results), 49 * dataset %>% length()),
    output_regression_test(results, output = "CP", filename = regFilename)
  )
  campsis_test(simulation, test, env = environment())
})