tests/testthat/test-simulate_events_logic.R

In campsis: Generic PK/PD Simulation Platform Campsis

library(testthat)

context("Test the events/interruption logic")

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

test_that("Simple interrutpions - No events", {
  if (skip_long_tests()) {
    return(TRUE)
  }
  model <- model_suite$testing$nonmem$advan4_trans4
  regFilename <- "simple_bolus" # Existing non-regression file (see testSimulateBolus.R)

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

  events <- Events()
  # 10 is part of the observations
  # 20.1 is not part of the observations
  event1 <- Event(name = "Event 1", times = c(10, 20.1), fun = function(inits) {
    # Don't do anything. Just return the inits data frame.
    return(inits)
  })
  events <- events %>% add(event1)

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

  # Without events
  simulation <- expression(simulate(model = model, dataset = dataset, dest = destEngine, events = NULL, seed = seed))
  test <- expression(
    output_regression_test(results, output = "CP", filename = regFilename)
  )
  campsis_test(simulation, test, env = environment())
})

test_that("Interruptions at doses times - BW covariate - No events", {
  if (skip_long_tests()) {
    return(TRUE)
  }
  model <- model_suite$testing$nonmem$advan4_trans4
  equation <- model %>% find(Equation("CL"))
  model <- model %>% replace(Equation("CL", paste0(equation@rhs, "*pow(BW/70, 0.75)")))
  regFilename <- "event_interruption_at_dose"

  dataset <- Dataset(2) %>%
    add(Bolus(time = 0, amount = 1000, compartment = 1)) %>%
    add(Bolus(time = 24, amount = 1000, compartment = 1)) %>%
    add(Observations(times = seq(0, 48, by = 5))) %>%
    add(Covariate(name = "BW", 70))

  events <- Events()
  # 10 is part of the observations
  # 24 is not part of the observations but is a bolus time
  # 34 is not part of the observations and not part of the doses times
  event1 <- Event(name = "Event 1", times = c(10, 24, 34), fun = function(inits) {
    # Don't do anything. Just return the inits data frame.
    return(inits)
  })
  events <- events %>% add(event1)

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

  # Without events
  simulation <- expression(simulate(model = model, dataset = dataset, dest = destEngine, events = NULL, seed = seed))
  test <- expression(
    output_regression_test(results, output = "CP", filename = regFilename)
  )
  campsis_test(simulation, test, env = environment())
})

test_that("Interruptions at doses times - BW covariate - IOV on KA - No events", {
  if (skip_long_tests()) {
    return(TRUE)
  }
  model <- model_suite$testing$nonmem$advan4_trans4
  equation <- model %>% find(Equation("CL"))
  model <- model %>% replace(Equation("CL", paste0(equation@rhs, "*pow(BW/70, 0.75)")))
  model <- model %>% replace(Equation("KA", "THETA_KA*exp(ETA_KA + IOV_KA)"))
  regFilename <- "event_interruption_at_dose_iov"

  dataset <- Dataset(2) %>%
    add(Bolus(time = 0, amount = 1000, compartment = 1)) %>%
    add(Bolus(time = 24, amount = 1000, compartment = 1)) %>%
    add(Observations(times = seq(0, 48, by = 5))) %>%
    add(Covariate(name = "BW", 70)) %>%
    add(IOV(colname = "IOV_KA", distribution = NormalDistribution(0, sd = 0.3)))

  # Uncomment these 2 lines to understand how IOV is exported!
  # dataset <- dataset %>% add(new("event_related_observations", times=c(10, 23, 24, 34), compartment=as.integer(NA)))
  # table <- dataset %>% export(dest="RxODE", event_related=TRUE)

  events <- Events()
  # 10 OBS TIME
  # 23 NOTHING, JUST BEFORE DOSE
  # 24 DOSE
  # 34 NOTHING
  event1 <- Event(name = "Event 1", times = c(10, 23, 24, 34), fun = function(inits) {
    # Don't do anything. Just return the inits data frame.
    return(inits)
  })
  events <- events %>% add(event1)

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

  # Without events
  simulation <- expression(simulate(model = model, dataset = dataset, dest = destEngine, events = NULL, seed = seed))
  test <- expression(
    output_regression_test(results, output = "CP", filename = regFilename)
  )
  campsis_test(simulation, test, env = environment())
})


test_that("Simulate initial conditions + events", {
  if (skip_long_tests()) {
    return(TRUE)
  }
  model <- model_suite$testing$nonmem$advan3_trans4
  model <- model %>% add(InitialCondition(compartment = 1, rhs = "1000"))

  regFilename <- "initial_conditions"

  dataset <- Dataset(3)
  dataset <- dataset %>% add(Observations(times = seq(0, 72, by = 1)))

  events <- Events()
  event1 <- Event(name = "Dummy event", times = c(0, 10), fun = function(inits) {
    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 %>% dplyr::filter(TIME >= 5), output = "CP", filename = regFilename)
  )
  campsis_test(simulation, test, env = environment())
})

test_that("Simulate multiple arms + events", {
  if (skip_long_tests()) {
    return(TRUE)
  }
  model <- model_suite$testing$nonmem$advan4_trans4

  regFilename <- "event_in_multiple_arms"

  dataset <- Dataset()
  # Treatment arm 1
  arm1 <- Arm(id = 1, subjects = 2) %>%
    add(Bolus(time = c(0, 24, 48), amount = 1000)) %>%
    add(Observations(times = seq(0, 72, by = 5)))

  # Treatment arm 2
  arm2 <- Arm(id = 2, subjects = 2) %>%
    add(Bolus(time = c(5, 29, 53), amount = 2000)) %>%
    add(Observations(times = seq(0, 77, by = 6)))

  dataset <- dataset %>% add(c(arm1, arm2))

  events <- Events()
  event1 <- Event(name = "Dummy event", times = c(0, 5, 20, 29, 40, 48), fun = function(inits) {
    return(inits)
  })
  events <- events %>% add(event1)

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

  # Without events
  simulation <- expression(simulate(model = model, dataset = dataset, dest = destEngine, events = NULL, seed = seed))
  test <- expression(
    output_regression_test(results, output = "CP", filename = regFilename)
  )
  campsis_test(simulation, test, env = environment())
})