tests/testthat/test-simulate_events.R

In campsis: Generic PK/PD Simulation Platform Campsis

library(testthat)

context("Test the simulate method with events")

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

test_that("Clear central compartment events", {
  if (skip_long_tests()) {
    return(TRUE)
  }
  model <- model_suite$testing$nonmem$advan4_trans4
  regFilename <- "clear_central_event"

  dataset <- Dataset(3) %>%
    add(Bolus(time = 0, amount = 1000, compartment = 1)) %>%
    add(Observations(times = seq(0, 24, by = 0.5)))

  events <- Events()
  event1 <- Event(name = "Event 1", times = c(15), fun = function(inits) {
    inits$A_CENTRAL <- 0
    return(inits)
  })
  events <- events %>% add(event1)

  simulation <- expression(simulate(model = model, dataset = dataset, dest = destEngine, events = events, seed = seed))
  test <- expression(
    output_regression_test(results, output = "CP", filename = regFilename),
    spaghettiPlot(results, "CP") # Still drug in A_PERIPHERAL
  )
  campsis_test(simulation, test, env = environment())
})

test_that("Give daily dose in absortion", {
  if (skip_long_tests()) {
    return(TRUE)
  }
  model <- model_suite$testing$nonmem$advan4_trans4
  regFilename <- "event_daily_dose"

  dataset <- Dataset(3) %>%
    add(Observations(times = seq(0, 24 * 7, by = 4)))

  events <- Events()
  event1 <- Event(name = "Event 1", times = seq(0, 24 * 6, by = 24), fun = function(inits) {
    inits$A_DEPOT <- inits$A_DEPOT + 1000
    return(inits)
  })
  events <- events %>% add(event1)

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

test_that("Daily dose in dataset + daily dose through events", {
  if (skip_long_tests()) {
    return(TRUE)
  }
  model <- model_suite$testing$nonmem$advan4_trans4
  regFilename <- "event_daily_dose"

  dataset <- Dataset(3) %>%
    add(Bolus(time = seq(0, 24 * 6, by = 24), amount = 500)) %>%
    add(Observations(times = seq(0, 24 * 7, by = 4)))

  events <- Events()
  event1 <- Event(name = "Half daily dose", times = seq(0, 24 * 6, by = 24), fun = function(inits) {
    inits$A_DEPOT <- inits$A_DEPOT + 500
    return(inits)
  })
  events <- events %>% add(event1)

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

test_that("Body weight as an event covariate", {
  if (skip_long_tests()) {
    return(TRUE)
  }
  model <- model_suite$testing$nonmem$advan2_trans2
  equation <- model %>% find(Equation("CL"))
  model <- model %>% replace(Equation("CL", paste0(equation@rhs, "*pow(BW/70, 0.75)")))
  regFilename <- "event_varying_bw"

  dataset <- Dataset(3)
  for (day in 0:2) {
    dataset <- dataset %>% add(Bolus(time = day * 24, amount = 1000))
  }
  dataset <- dataset %>% add(Observations(times = seq(0, 24 * 2, by = 1)))
  dataset <- dataset %>% add(EventCovariate("BW", 100))

  events <- Events()
  event1 <- Event(name = "Event 1", times = 15, fun = function(inits) {
    inits$BW <- 60
    return(inits)
  })
  event2 <- Event(name = "Event 2", times = 30, fun = function(inits) {
    inits$BW <- 30
    return(inits)
  })
  events <- events %>% add(event1) %>% add(event2)

  simulation <- expression(simulate(
    model = model,
    dataset = dataset,
    dest = destEngine,
    events = events,
    seed = seed,
    outvars = "BW"
  ))
  test <- expression(
    output_regression_test(results, output = "CP", filename = regFilename),
    spaghettiPlot(results, "CP")
  )
  campsis_test(simulation, test, env = environment())
})

test_that("Dose adaptation based on Ctrough", {
  if (skip_long_tests()) {
    return(TRUE)
  }
  model <- model_suite$testing$nonmem$advan2_trans2
  regFilename <- "dose_adaptation_ctrough"

  dataset <- Dataset(5)
  days <- 7
  dataset <- dataset %>% add(Observations(times = seq(0, 24 * days, by = 1)))
  dataset <- dataset %>% add(EventCovariate("DOSE", 1500))

  events <- Events()
  event1 <- Event(name = "Dose adaptation", times = (seq_len(days) - 1) * 24, fun = function(inits) {
    inits$DOSE <- ifelse(inits$CP > 5, inits$DOSE * 0.75, inits$DOSE)
    inits$A_DEPOT <- inits$A_DEPOT + inits$DOSE
    return(inits)
  })
  events <- events %>% add(event1)

  simulation <- expression(simulate(
    model = model,
    dataset = dataset,
    dest = destEngine,
    events = events,
    seed = seed,
    outvars = "DOSE"
  ))
  test <- expression(
    output_regression_test(results, output = c("CP", "DOSE"), filename = regFilename),
    spaghettiPlot(results, "CP")
  )
  campsis_test(simulation, test, env = environment())
})