tests/testthat/test-addTransit.R

In nlmixr2lib: A Model Library for 'nlmixr2'

test_that("addTransit adds transit compartment", {
  modelTest <- readModelDb("PK_1cmt_des") |> addTransit(3)
  modelTest <- rxode2::assertRxUi(modelTest)
  suppressMessages(modelUpdate <- addTransit(modelTest, 1))
  # check for lktr1 in ini block
  temp <- rxode2::assertRxUi(modelUpdate)
  temp2 <- temp$iniDf
  expect_equal("lktr" %in% temp2$name, TRUE)

  # check for ktr in model block
  suppressMessages(kaLine <- rxode2::modelExtract(modelUpdate, "ktr", lines = TRUE))
  expect_equal(grepl("\\s*^ktr", kaLine), TRUE)
})


# Test if the function throws an error when invalid input for 'central' is provided
test_that("addTransit throws an error with invalid 'central'", {
  expect_error(addTransit(readModelDb("PK_2cmt_des"), 3, "cent", "depot"), "'cent' compartment is not in the model")
})

# Test if the function throws an error when invalid input for 'transit' is provided
test_that("addTransit throws an error with invalid 'transit'", {
  expect_error(addTransit(readModelDb("PK_2cmt_des"), -1), "Assertion on 'ntransit' failed: Element 1 is not >= 1")
})

# Test if the function adds transit compartments correctly when 'depot' is present
test_that("addTransit adds transit compartments correctly with 'depot'", {
  modelTest <- readModelDb("PK_1cmt_des") |> addTransit(3)
  modelTest <- rxode2::assertRxUi(modelTest)
  modelUpdate <- addTransit(modelTest, 3)
  temp <- rxode2::assertRxUi(modelUpdate)
  mv <- rxode2::rxModelVars(temp)
  expect_equal("transit1" %in% mv$state, TRUE)
  expect_equal("transit2" %in% mv$state, TRUE)
  expect_equal("transit3" %in% mv$state, TRUE)
})

# Test if the function adds transit compartments  when 'depot' is not present
test_that("addTransit does not add transit compartments  without 'depot'", {
  expect_warning(addTransit(readModelDb("PK_2cmt_no_depot"), 1), "'depot' added to model for transit model")
})

test_that("extreme model cases", {

  f <- function() {
    model({
      d/dt(depot) <- -ka*depot
      d/dt(central) <- ka*depot-kel*central
      Cc <- central / vc
    })
  }

  f <- rxode2::rxode2(f)

  expect_error(f %>% addTransit(4), NA)
  expect_warning(f %>% addTransit(4), NA)

  f <- function() {
    ini({
      e ~ 0.1
    })
    model({
      ka <- exp(e)
      d/dt(depot) <- -ka*depot
      d/dt(central) <- ka*depot-kel*central
      Cc <- central / vc
    })
  }

  f <- rxode2::rxode2(f)

  omega <- f$omega

  expect_error(f %>% addTransit(4), NA)
  expect_warning(f %>% addTransit(4), NA)

  tmp <- f %>% addTransit(4)

  expect_equal(omega, tmp$omega)

})