tests/testthat/testSimulateEventsLogic.R

In Calvagone/campsis: Generic PK/PD Simulation Platform CAMPSIS

library(testthat)

context("Test the events/interruption logic")

seed <- 1
source(paste0("", "testUtils.R"))

test_that(getTestName("Simple interrutpions - No events"), {
  if (skipLongTest) 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(
    outputRegressionTest(results, output="CP", filename=regFilename)
  )
  campsisTest(simulation, test, env=environment())
  
  # Without events
  simulation <- expression(simulate(model=model, dataset=dataset, dest=destEngine, events=NULL, seed=seed))
  test <- expression(
    outputRegressionTest(results, output="CP", filename=regFilename)
  )
  campsisTest(simulation, test, env=environment())
})

test_that(getTestName("Interruptions at doses times - BW covariate - No events"), {
  if (skipLongTest) 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(
    outputRegressionTest(results, output="CP", filename=regFilename)
  )
  campsisTest(simulation, test, env=environment())
  
  # Without events
  simulation <- expression(simulate(model=model, dataset=dataset, dest=destEngine, events=NULL, seed=seed))
  test <- expression(
    outputRegressionTest(results, output="CP", filename=regFilename)
  )
  campsisTest(simulation, test, env=environment())
})

test_that(getTestName("Interruptions at doses times - BW covariate - IOV on KA - No events"), {
  if (skipLongTest) 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(
    outputRegressionTest(results, output="CP", filename=regFilename)
  )
  campsisTest(simulation, test, env=environment())
  
  # Without events
  simulation <- expression(simulate(model=model, dataset=dataset, dest=destEngine, events=NULL, seed=seed))
  test <- expression(
    outputRegressionTest(results, output="CP", filename=regFilename)
  )
  campsisTest(simulation, test, env=environment())
})


test_that(getTestName("Simulate initial conditions + events"), {
  if (skipLongTest) 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(
    outputRegressionTest(results %>% dplyr::filter(TIME >=5), output="CP", filename=regFilename)
  )
  campsisTest(simulation, test, env=environment())
})

test_that(getTestName("Simulate multiple arms + events"), {
  if (skipLongTest) 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(
    outputRegressionTest(results, output="CP", filename=regFilename)
  )
  campsisTest(simulation, test, env=environment())
  
  # Without events
  simulation <- expression(simulate(model=model, dataset=dataset, dest=destEngine, events=NULL, seed=seed))
  test <- expression(
    outputRegressionTest(results, output="CP", filename=regFilename)
  )
  campsisTest(simulation, test, env=environment())
})