tests/testthat/test-treatment_entry.R

In campsis: Generic PK/PD Simulation Platform Campsis

library(testthat)

context("Test all types of treatment entries")

test_that("Bolus is working correctly", {
  bolus <- Bolus(time = 0, amount = 1000, wrap = F)
  expect_equal(bolus@time, 0)
  expect_equal(bolus@amount, 1000)
  expect_equal(bolus %>% get_name(), "BOLUS [TIME=0, CMT=DEFAULT]")
})

test_that("Infusion is working correctly", {
  infusion <- Infusion(time = 0, amount = 1000, wrap = F)
  expect_equal(infusion@time, 0)
  expect_equal(infusion@amount, 1000)
  expect_equal(infusion %>% get_name(), "INFUSION [TIME=0, CMT=DEFAULT]")
})

test_that("Infusion errors", {
  expect_error(Infusion(time = 0)) # amount is missing
})

test_that("Infusion time is negative", {
  expect_error(Infusion(time = -1, amount = 100), regexp = "Some values in slot 'time' are negative")
})


test_that("Is treatment entry test", {
  expect_true(is(Bolus(time = 0, amount = 100), "treatment_entry"))
})

test_that("sample method for bolus is working well", {
  bolus <- Bolus(time = 0, amount = 1000, f = 0.6, lag = ConstantDistribution(2), wrap = F)
  res <- bolus %>% sample(n = as.integer(10))
  expect_equal(res$ID, seq_len(10))
  expect_equal(unique(res$AMT), 1000 * 0.6)
  expect_equal(unique(res$TIME), 0 + 2)
})

test_that("sample method for infusion is working well", {
  infusion <- Infusion(time = 0, amount = 1000, duration = 2, wrap = F)
  res <- infusion %>% sample(n = as.integer(10))
  expect_equal(res$ID, seq_len(10))
  expect_equal(unique(res$RATE), 1000 / 2)

  infusion <- Infusion(time = 0, amount = 1000, rate = 200, wrap = F)
  res <- infusion %>% sample(n = as.integer(10))
  expect_equal(res$ID, seq_len(10))
  expect_equal(unique(res$RATE), 200)
})

test_that("'time' vector or 'ii' and 'addl' are equivalent (boluses)", {
  boluses1 <- Bolus(time = c(0, 24, 48), amount = 100, wrap = F)
  expect_equal(boluses1 %>% length(), 3)

  boluses2 <- Bolus(time = 0, amount = 100, ii = 24, addl = 2, wrap = F)
  expect_equal(boluses2 %>% length(), 3)

  expect_equal(boluses1, boluses2)

  bolus1 <- Bolus(time = 24, amount = 100, wrap = F)
  bolus2 <- Bolus(time = 24, amount = 100, ii = 24, addl = 0, wrap = F)

  expect_equal(bolus1, bolus2)
})

test_that("'time' vector or 'ii' and 'addl' are equivalent (infusions)", {
  infusions1 <- Infusion(time = c(0, 24, 48), amount = 100, wrap = F)
  expect_equal(infusions1 %>% length(), 3)

  infusions2 <- Infusion(time = 0, amount = 100, ii = 24, addl = 2, wrap = F)
  expect_equal(infusions2 %>% length(), 3)

  expect_equal(infusions1, infusions2)

  infusion1 <- Infusion(time = 24, amount = 100, wrap = F)
  infusion2 <- Infusion(time = 24, amount = 100, ii = 24, addl = 0, wrap = F)

  expect_equal(infusion1, infusion2)
})

test_that("assertions on 'ii' and 'addl' work well", {
  expect_error(Bolus(time = c(0), amount = 100, ii = 24), regexp = "addl can't be NULL if ii is specified")
  expect_error(Infusion(time = c(0), amount = 100, ii = 24), regexp = "addl can't be NULL if ii is specified")
  expect_error(Bolus(time = c(0), amount = 100, addl = 0), regexp = "ii can't be NULL if addl is specified")
  expect_error(
    Bolus(time = c(24, 48), amount = 100, ii = 24, addl = 0),
    regexp = "time must be a single numeric value if used with ii and addl"
  )
  expect_error(Bolus(time = 0, amount = 100, ii = 24, addl = -2), regexp = "addl must be positive")
  expect_error(Bolus(time = 0, amount = 100, ii = -2, addl = 2), regexp = "ii must be higher than 0")
  expect_error(Bolus(time = 0, amount = 100, ii = 24, addl = 5.2), regexp = "addl must be a single integer value")
  expect_error(Bolus(time = 0, amount = 100, ii = c(24, 48), addl = 2), regexp = "ii must be a single numeric value")
})

test_that("Bolus or infusion wrappers", {
  infusion <- Infusion(time = 0, amount = 100, compartment = "CENTRAL", ii = 24, addl = 6, duration = 2, ref = "Admin1")
  expect_equal(as.character(class(infusion)), "infusion_wrapper")
  expect_equal(infusion %>% get_name(), "INFUSION WRAPPER [REF=Admin1]")
  expect_equal(infusion@ii, 24)
  expect_equal(infusion@addl, 6)
  expect_equal(length(infusion@duration), 1)

  bolus <- Bolus(
    time = 0,
    amount = 100,
    compartment = c("DEPOT1", "DEPOT2"),
    ii = 24,
    addl = 6,
    f = c(0.7, 0.3),
    ref = "Admin1"
  )
  expect_equal(as.character(class(bolus)), "bolus_wrapper")
  expect_equal(bolus %>% get_name(), "BOLUS WRAPPER [REF=Admin1]")
  expect_equal(bolus@ii, 24)
  expect_equal(bolus@addl, 6)
  expect_equal(length(bolus@f), 2)

  dataset <- Dataset(3) %>%
    add(bolus) %>%
    add(infusion)

  entries <- length(dataset@arms@list[[1]]@protocol@treatment@list)
  expect_equal(entries, 2)

  # After unwrap
  dataset_ <- dataset %>%
    unwrap_treatment()

  # update_amount, updateDosingInterval, update_addl

  entries <- length(dataset_@arms@list[[1]]@protocol@treatment@list)
  expect_equal(entries, 14)
})