tests/testthat/test-simulate_time_varying_covariates.R

In campsis: Generic PK/PD Simulation Platform Campsis

library(testthat)

context("Test the simulate method with timevarying covariates")

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

test_that("Body weight as a true time varying covariate", {
  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) %>%
    add(Bolus(time = 0, amount = 1000, ii = 24, addl = 2)) %>%
    add(Observations(times = seq(0, 24 * 2, by = 1))) %>%
    add(TimeVaryingCovariate("BW", data.frame(TIME = c(0, 15, 30), VALUE = c(100, 60, 30))))

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

test_that("Body weight as a true time varying covariate, 2 arms, individual body weights", {
  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_2arms_ind"

  bw1_1 <- data.frame(ID = 1, TIME = c(0), VALUE = c(70)) # Constant
  bw1_2 <- data.frame(ID = 2, TIME = c(0, 24), VALUE = c(100, 90))
  bw2_1 <- data.frame(ID = 1, TIME = c(0, 12, 25, 36), VALUE = c(90, 80, 70, 60))
  bw2_2 <- data.frame(ID = 2, TIME = c(0, 12, 25, 36), VALUE = c(50, 40, 30, 20))

  arm1 <- Arm(id = 1, subjects = 2) %>%
    add(Bolus(time = 0, amount = 1000, ii = 24, addl = 2)) %>%
    add(Observations(times = seq(0, 24 * 2, by = 1))) %>%
    add(TimeVaryingCovariate("BW", dplyr::bind_rows(bw1_1, bw1_2)))

  arm2 <- Arm(id = 2, subjects = 2) %>%
    add(Bolus(time = 0, amount = 1000, ii = 24, addl = 2)) %>%
    add(Observations(times = seq(0, 24 * 2, by = 1))) %>%
    add(TimeVaryingCovariate("BW", dplyr::bind_rows(bw2_1, bw2_2)))

  ds <- Dataset() %>% add(c(arm1, arm2))

  simulation <- expression(simulate(
    model = model %>% disable("IIV"),
    dataset = ds,
    dest = destEngine,
    seed = seed,
    outvars = "BW",
    settings = Settings(NOCB(variables = "BW"))
  ))
  test <- expression(
    spaghettiPlot(results, "CP", "ID"),
    spaghettiPlot(results, "BW", "ID"),
    output_regression_test(results, output = "CP", filename = regFilename)
  )
  campsis_test(simulation, test, env = environment())
})