tests/testthat/test-show_method.R

In campsis: Generic PK/PD Simulation Platform Campsis

library(testthat)

context("Test the show method applied on a dataset")

test_that("Applying method show on a few datasets works as expected", {
  # Dataset with dose adaptation, CMT not specified (1)
  dataset <- Dataset(2) %>%
    add(Bolus(time = seq(0, 6) * 24, amount = 0.5)) %>% # 0.5mg / kg
    add(Observations(times = seq(0, 7 * 24, by = 4))) %>%
    add(Covariate("WT", c(100, 50))) %>%
    add(DoseAdaptation("AMT*WT"))
  #show(dataset)
  expect_true("-> Dose adaptation (CMT=ALL): AMT*WT" %in% capture.output(show(dataset)))

  # Dataset with dose adaptation, CMT=1 (2)
  times <- seq(0, 7 * 24, by = 4)
  dataset <- Dataset(2) %>%
    add(Bolus(time = 0, amount = 0.5, compartment = 1, ii = 24, addl = 6)) %>%
    add(Bolus(time = 0, amount = 1000, compartment = 5)) %>%
    add(Observations(times = times)) %>%
    add(Covariate("WT", c(100, 50))) %>%
    add(Covariate("WT2", c(100, 50))) %>%
    add(DoseAdaptation("AMT*WT", compartments = 1))
  #show(dataset)
  expect_true("-> Dose adaptation (CMT=1): AMT*WT" %in% capture.output(show(dataset)))

  # Dataset with an Infusion, IOV
  dataset <- Dataset() %>%
    add(Infusion(time = 0, amount = 1000, compartment = 1)) %>%
    add(Observations(times = seq(0, 24, by = 0.5))) %>%
    add(IOV("IOV_KA", NormalDistribution(0, 1)))
  #show(dataset)
  expect_true("-> Adm. times (infusion into CMT=1): 0 (1000)" %in% capture.output(show(dataset)))
  expect_true("-> Treatment IOV: IOV_KA" %in% capture.output(show(dataset)))

  # Dataset with 2 arms and timevarying covariates
  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 = 2000, 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))
  #show(ds)
  expect_true("Arm 1 (N=2)" %in% capture.output(show(ds)))
  expect_true("Arm 2 (N=2)" %in% capture.output(show(ds)))
  expect_true("Time-varying covariates: BW" %in% capture.output(show(ds)))

  # Dataset with occasions, multiple ascending doses
  ds <- Dataset() %>%
    add(Bolus(time = 0, amount = 100)) %>%
    add(Bolus(time = 24, amount = 100)) %>%
    add(Bolus(time = 48, amount = 200)) %>%
    add(Bolus(time = 72, amount = 200)) %>%
    add(Bolus(time = 96, amount = 300)) %>%
    add(Bolus(time = 120, amount = 400)) %>%
    add(Observations(times = seq(0, 60, by = 10))) %>%
    add(Occasion("MY_OCC", values = c(1, 2, 3), doseNumbers = c(1, 2, 3)))
  #show(ds)
  expect_true(
    "-> Adm. times (bolus into DEFAULT): 0 (100),24,48 (200),72,96 (300),120 (400)" %in% capture.output(show(ds))
  )
  expect_true("-> Treatment occasions: MY_OCC" %in% capture.output(show(ds)))

  # Dataset with observations-only and event-related covariates
  ds <- Dataset(3) %>%
    add(Covariate("BAS", 0.02)) %>%
    add(Covariate("WT", 70)) %>%
    add(Observations(0:336)) %>%
    add(Covariate("ROUT", 0)) %>%
    add(EventCovariate("CURRENT_DOSE", 0)) %>%
    add(EventCovariate("LAST_DOSE", 0.1))
  #show(ds)
  expect_true("Covariates: BAS,WT,ROUT" %in% capture.output(show(ds)))
  expect_true("Event-related covariates: CURRENT_DOSE,LAST_DOSE" %in% capture.output(show(ds)))

  # Dataset with covariates and NHANES bootstrap
  ds <- Dataset(subjects = 10) %>%
    add(Bolus(time = 0, amount = 1000, compartment = 1, ii = 24, addl = 0)) %>%
    add(Observations(seq(0, 24, by = 1))) %>%
    add(Covariate("HELLO", 0)) %>%
    add(Bootstrap(data = campsis::nhanes, replacement = TRUE, random = TRUE))

  expect_true("Covariates: HELLO" %in% capture.output(show(ds)))
  expect_true("Bootstrap: BS_ID,SEX,AGE,BW,BMI,HT" %in% capture.output(show(ds)))

  # Dataset without covariates and NHANES bootstrap
  ds <- Dataset(subjects = 10) %>%
    add(Bolus(time = 0, amount = 1000, compartment = 1, ii = 24, addl = 0)) %>%
    add(Observations(seq(0, 24, by = 1))) %>%
    add(Bootstrap(data = campsis::nhanes, replacement = TRUE, random = TRUE))

  expect_true(!("No covariates" %in% capture.output(show(ds))))
  expect_true("Bootstrap: BS_ID,SEX,AGE,BW,BMI,HT" %in% capture.output(show(ds)))
})