Nothing
test_that('tpi_selector matches published example.', {
# Reproduce decisions conveyed in Table 1 in Ji et al. (2007)
# at https://doi.org/10.1177/1740774507079442
num_doses <- 5
target <- 0.3
model <- get_tpi(num_doses = num_doses, target = target,
k1 = 1, k2 = 1.5, exclusion_certainty = 0.95)
# Tests at dose 1
# Three patients treated
fit <- model %>% fit('1NNN')
expect_equal(recommended_dose(fit), 2)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1TTT')
expect_true(is.na(recommended_dose(fit)))
expect_false(continue(fit))
expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit)))
# Six patients treated
fit <- model %>% fit('1NNN 1NNN')
expect_equal(recommended_dose(fit), 2)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNN 1NNT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNN 1NTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNN 1TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNT 1TTT')
expect_true(is.na(recommended_dose(fit)))
expect_false(continue(fit))
expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit)))
fit <- model %>% fit('1NTT 1TTT')
expect_true(is.na(recommended_dose(fit)))
expect_false(continue(fit))
expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit)))
fit <- model %>% fit('1TTT 1TTT')
expect_true(is.na(recommended_dose(fit)))
expect_false(continue(fit))
expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit)))
# Nine patients treated
fit <- model %>% fit('1NNN 1NNN 1NNN')
expect_equal(recommended_dose(fit), 2)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNN 1NNN 1NNT')
expect_equal(recommended_dose(fit), 2)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNN 1NNN 1NTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNN 1NNN 1TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNN 1NNT 1TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNN 1NTT 1TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNN 1TTT 1TTT')
expect_true(is.na(recommended_dose(fit)))
expect_false(continue(fit))
expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit)))
fit <- model %>% fit('1NNT 1TTT 1TTT')
expect_true(is.na(recommended_dose(fit)))
expect_false(continue(fit))
expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit)))
fit <- model %>% fit('1NTT 1TTT 1TTT')
expect_true(is.na(recommended_dose(fit)))
expect_false(continue(fit))
expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit)))
fit <- model %>% fit('1TTT 1TTT 1TTT')
expect_true(is.na(recommended_dose(fit)))
expect_false(continue(fit))
expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit)))
# Twelve patients treated
fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN')
expect_equal(recommended_dose(fit), 2)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNN 1NNN 1NNN 1NNT')
expect_equal(recommended_dose(fit), 2)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNN 1NNN 1NNN 1NTT')
expect_equal(recommended_dose(fit), 2)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNN 1NNN 1NNN 1TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNN 1NNN 1NNT 1TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNN 1NNN 1NTT 1TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNN 1NNN 1TTT 1TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('1NNN 1NNT 1TTT 1TTT')
expect_true(is.na(recommended_dose(fit)))
expect_false(continue(fit))
expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit)))
fit <- model %>% fit('1NNN 1NTT 1TTT 1TTT')
expect_true(is.na(recommended_dose(fit)))
expect_false(continue(fit))
expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit)))
fit <- model %>% fit('1NNN 1TTT 1TTT 1TTT')
expect_true(is.na(recommended_dose(fit)))
expect_false(continue(fit))
expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit)))
fit <- model %>% fit('1NNT 1TTT 1TTT 1TTT')
expect_true(is.na(recommended_dose(fit)))
expect_false(continue(fit))
expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit)))
fit <- model %>% fit('1NTT 1TTT 1TTT 1TTT')
expect_true(is.na(recommended_dose(fit)))
expect_false(continue(fit))
expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit)))
fit <- model %>% fit('1TTT 1TTT 1TTT 1TTT')
expect_true(is.na(recommended_dose(fit)))
expect_false(continue(fit))
expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit)))
# Tests at dose 2
# Three patients treated
fit <- model %>% fit('2NNN')
expect_equal(recommended_dose(fit), 3)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNT')
expect_equal(recommended_dose(fit), 2)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE))
# Six patients treated
fit <- model %>% fit('2NNN 2NNN')
expect_equal(recommended_dose(fit), 3)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNN 2NNT')
expect_equal(recommended_dose(fit), 2)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNN 2NTT')
expect_equal(recommended_dose(fit), 2)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNN 2TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNT 2TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE))
fit <- model %>% fit('2NTT 2TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE))
fit <- model %>% fit('2TTT 2TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE))
# Nine patients treated
fit <- model %>% fit('2NNN 2NNN 2NNN')
expect_equal(recommended_dose(fit), 3)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNN 2NNN 2NNT')
expect_equal(recommended_dose(fit), 3)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNN 2NNN 2NTT')
expect_equal(recommended_dose(fit), 2)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNN 2NNN 2TTT')
expect_equal(recommended_dose(fit), 2)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNN 2NNT 2TTT')
expect_equal(recommended_dose(fit), 2)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNN 2NTT 2TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNN 2TTT 2TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE))
fit <- model %>% fit('2NNT 2TTT 2TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE))
fit <- model %>% fit('2NTT 2TTT 2TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE))
fit <- model %>% fit('2TTT 2TTT 2TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE))
# Twelve patients treated
fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN')
expect_equal(recommended_dose(fit), 3)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNN 2NNN 2NNN 2NNT')
expect_equal(recommended_dose(fit), 3)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNN 2NNN 2NNN 2NTT')
expect_equal(recommended_dose(fit), 3)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNN 2NNN 2NNN 2TTT')
expect_equal(recommended_dose(fit), 2)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNN 2NNN 2NNT 2TTT')
expect_equal(recommended_dose(fit), 2)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNN 2NNN 2NTT 2TTT')
expect_equal(recommended_dose(fit), 2)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNN 2NNN 2TTT 2TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('2NNN 2NNT 2TTT 2TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE))
fit <- model %>% fit('2NNN 2NTT 2TTT 2TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE))
fit <- model %>% fit('2NNN 2TTT 2TTT 2TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE))
fit <- model %>% fit('2NNT 2TTT 2TTT 2TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE))
fit <- model %>% fit('2NTT 2TTT 2TTT 2TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE))
fit <- model %>% fit('2TTT 2TTT 2TTT 2TTT')
expect_equal(recommended_dose(fit), 1)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE))
# Tests at top dose (i.e. escalation impossible)
# Three patients treated
fit <- model %>% fit('5NNN')
expect_equal(recommended_dose(fit), 5)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNT')
expect_equal(recommended_dose(fit), 5)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5TTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE))
# Six patients treated
fit <- model %>% fit('5NNN 5NNN')
expect_equal(recommended_dose(fit), 5)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNN 5NNT')
expect_equal(recommended_dose(fit), 5)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNN 5NTT')
expect_equal(recommended_dose(fit), 5)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNN 5TTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNT 5TTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE))
fit <- model %>% fit('5NTT 5TTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE))
fit <- model %>% fit('5TTT 5TTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE))
# Nine patients treated
fit <- model %>% fit('5NNN 5NNN 5NNN')
expect_equal(recommended_dose(fit), 5)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNN 5NNN 5NNT')
expect_equal(recommended_dose(fit), 5)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNN 5NNN 5NTT')
expect_equal(recommended_dose(fit), 5)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNN 5NNN 5TTT')
expect_equal(recommended_dose(fit), 5)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNN 5NNT 5TTT')
expect_equal(recommended_dose(fit), 5)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNN 5NTT 5TTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNN 5TTT 5TTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE))
fit <- model %>% fit('5NNT 5TTT 5TTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE))
fit <- model %>% fit('5NTT 5TTT 5TTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE))
fit <- model %>% fit('5TTT 5TTT 5TTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE))
# Twelve patients treated
fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN')
expect_equal(recommended_dose(fit), 5)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNN 5NNN 5NNN 5NNT')
expect_equal(recommended_dose(fit), 5)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNN 5NNN 5NNN 5NTT')
expect_equal(recommended_dose(fit), 5)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNN 5NNN 5NNN 5TTT')
expect_equal(recommended_dose(fit), 5)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNN 5NNN 5NNT 5TTT')
expect_equal(recommended_dose(fit), 5)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNN 5NNN 5NTT 5TTT')
expect_equal(recommended_dose(fit), 5)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNN 5NNN 5TTT 5TTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('5NNN 5NNT 5TTT 5TTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE))
fit <- model %>% fit('5NNN 5NTT 5TTT 5TTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE))
fit <- model %>% fit('5NNN 5TTT 5TTT 5TTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE))
fit <- model %>% fit('5NNT 5TTT 5TTT 5TTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE))
fit <- model %>% fit('5NTT 5TTT 5TTT 5TTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE))
fit <- model %>% fit('5TTT 5TTT 5TTT 5TTT')
expect_equal(recommended_dose(fit), 4)
expect_true(continue(fit))
expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE))
})
test_that('tpi_selector supports correct interface.', {
num_doses <- 5
target <- 0.3
model_fitter <- get_tpi(num_doses = num_doses, target = target,
k1 = 1, k2 = 1.5, exclusion_certainty = 0.9)
# Example 1, using outcome string
x <- fit(model_fitter, '1NNN 2NTT')
expect_equal(tox_target(x), 0.3)
expect_true(is.numeric(tox_target(x)))
expect_equal(num_patients(x), 6)
expect_true(is.integer(num_patients(x)))
expect_equal(cohort(x), c(1,1,1, 2,2,2))
expect_true(is.integer(cohort(x)))
expect_equal(length(cohort(x)), num_patients(x))
expect_equal(doses_given(x), c(1,1,1, 2,2,2))
expect_true(is.integer(doses_given(x)))
expect_equal(length(doses_given(x)), num_patients(x))
expect_equal(tox(x), c(0,0,0, 0,1,1))
expect_true(is.integer(tox(x)))
expect_equal(length(tox(x)), num_patients(x))
expect_true(all((model_frame(x) - data.frame(patient = c(1,2,3,4,5,6),
cohort = c(1,1,1,2,2,2),
dose = c(1,1,1,2,2,2),
tox = c(0,0,0,0,1,1))) == 0))
expect_equal(nrow(model_frame(x)), num_patients(x))
expect_equal(num_doses(x), 5)
expect_true(is.integer(num_doses(x)))
expect_equal(dose_indices(x), 1:5)
expect_true(is.integer(dose_indices(x)))
expect_equal(length(dose_indices(x)), num_doses(x))
expect_equal(recommended_dose(x), 1)
expect_true(is.integer(recommended_dose(x)))
expect_equal(length(recommended_dose(x)), 1)
expect_equal(continue(x), TRUE)
expect_true(is.logical(continue(x)))
expect_equal(n_at_dose(x), c(3,3,0,0,0))
expect_true(is.integer(n_at_dose(x)))
expect_equal(length(n_at_dose(x)), num_doses(x))
expect_equal(n_at_dose(x, dose = 0), 0)
expect_true(is.integer(n_at_dose(x, dose = 0)))
expect_equal(length(n_at_dose(x, dose = 0)), 1)
expect_equal(n_at_dose(x, dose = 1), 3)
expect_true(is.integer(n_at_dose(x, dose = 1)))
expect_equal(length(n_at_dose(x, dose = 1)), 1)
expect_equal(n_at_dose(x, dose = 'recommended'), 3)
expect_true(is.integer(n_at_dose(x, dose = 'recommended')))
expect_equal(length(n_at_dose(x, dose = 'recommended')), 1)
expect_equal(n_at_recommended_dose(x), 3)
expect_true(is.integer(n_at_recommended_dose(x)))
expect_equal(length(n_at_recommended_dose(x)), 1)
expect_equal(is_randomising(x), FALSE)
expect_true(is.logical(is_randomising(x)))
expect_equal(length(is_randomising(x)), 1)
expect_equal(unname(prob_administer(x)), c(0.5,0.5,0,0,0))
expect_true(is.numeric(prob_administer(x)))
expect_equal(length(prob_administer(x)), num_doses(x))
expect_equal(tox_at_dose(x), c(0,2,0,0,0))
expect_true(is.integer(tox_at_dose(x)))
expect_equal(length(tox_at_dose(x)), num_doses(x))
expect_true(is.numeric(empiric_tox_rate(x)))
expect_equal(length(empiric_tox_rate(x)), num_doses(x))
expect_true(is.numeric(mean_prob_tox(x)))
expect_equal(length(mean_prob_tox(x)), num_doses(x))
expect_true(is.numeric(median_prob_tox(x)))
expect_equal(length(median_prob_tox(x)), num_doses(x))
expect_true(is.logical(dose_admissible(x)))
expect_equal(length(dose_admissible(x)), num_doses(x))
expect_true(is.numeric(prob_tox_quantile(x, p = 0.9)))
expect_equal(length(prob_tox_quantile(x, p = 0.9)), num_doses(x))
expect_true(is.numeric(prob_tox_exceeds(x, 0.5)))
expect_equal(length(prob_tox_exceeds(x, 0.5)), num_doses(x))
expect_true(is.logical(supports_sampling(x)))
expect_error(prob_tox_samples(x))
expect_error(prob_tox_samples(x, tall = TRUE))
# Expect summary to not error. This is how that is tested, apparently:
expect_error(summary(x), NA)
expect_output(print(x))
expect_true(tibble::is_tibble(as_tibble(x)))
expect_true(nrow(as_tibble(x)) >= num_doses(x))
# Example 2, using trivial outcome string
x <- fit(model_fitter, '')
expect_equal(tox_target(x), 0.3)
expect_true(is.numeric(tox_target(x)))
expect_equal(num_patients(x), 0)
expect_true(is.integer(num_patients(x)))
expect_equal(cohort(x), integer(0))
expect_true(is.integer(cohort(x)))
expect_equal(length(cohort(x)), num_patients(x))
expect_equal(doses_given(x), integer(0))
expect_true(is.integer(doses_given(x)))
expect_equal(length(doses_given(x)), num_patients(x))
expect_equal(tox(x), integer(0))
expect_true(is.integer(tox(x)))
expect_equal(length(tox(x)), num_patients(x))
expect_equal(num_tox(x), 0)
expect_true(is.integer(num_tox(x)))
expect_equal(dose_indices(x), 1:5)
expect_true(is.integer(dose_indices(x)))
expect_equal(length(dose_indices(x)), num_doses(x))
mf <- model_frame(x)
expect_equal(nrow(mf), 0)
expect_equal(ncol(mf), 4)
expect_equal(num_doses(x), 5)
expect_true(is.integer(num_doses(x)))
expect_equal(recommended_dose(x), 1)
expect_true(is.integer(recommended_dose(x)))
expect_equal(length(recommended_dose(x)), 1)
expect_equal(continue(x), TRUE)
expect_true(is.logical(continue(x)))
expect_equal(n_at_dose(x), c(0,0,0,0,0))
expect_true(is.integer(n_at_dose(x)))
expect_equal(length(n_at_dose(x)), num_doses(x))
expect_equal(n_at_dose(x, dose = 0), 0)
expect_true(is.integer(n_at_dose(x, dose = 0)))
expect_equal(length(n_at_dose(x, dose = 0)), 1)
expect_equal(n_at_dose(x, dose = 1), 0)
expect_true(is.integer(n_at_dose(x, dose = 1)))
expect_equal(length(n_at_dose(x, dose = 1)), 1)
expect_equal(n_at_dose(x, dose = 'recommended'), 0)
expect_true(is.integer(n_at_dose(x, dose = 'recommended')))
expect_equal(length(n_at_dose(x, dose = 'recommended')), 1)
expect_equal(n_at_recommended_dose(x), 0)
expect_true(is.integer(n_at_recommended_dose(x)))
expect_equal(length(n_at_recommended_dose(x)), 1)
expect_equal(is_randomising(x), FALSE)
expect_true(is.logical(is_randomising(x)))
expect_equal(length(is_randomising(x)), 1)
expect_true(is.numeric(prob_administer(x)))
expect_equal(length(prob_administer(x)), num_doses(x))
expect_equal(tox_at_dose(x), c(0,0,0,0,0))
expect_true(is.integer(tox_at_dose(x)))
expect_equal(length(tox_at_dose(x)), num_doses(x))
expect_true(is.numeric(empiric_tox_rate(x)))
expect_equal(length(empiric_tox_rate(x)), num_doses(x))
expect_true(is.numeric(mean_prob_tox(x)))
expect_equal(length(mean_prob_tox(x)), num_doses(x))
expect_true(is.numeric(median_prob_tox(x)))
expect_equal(length(median_prob_tox(x)), num_doses(x))
expect_true(is.logical(dose_admissible(x)))
expect_equal(length(dose_admissible(x)), num_doses(x))
expect_true(is.numeric(prob_tox_quantile(x, p = 0.9)))
expect_equal(length(prob_tox_quantile(x, p = 0.9)), num_doses(x))
expect_true(is.numeric(prob_tox_exceeds(x, 0.5)))
expect_equal(length(prob_tox_exceeds(x, 0.5)), num_doses(x))
expect_true(is.logical(supports_sampling(x)))
expect_error(prob_tox_samples(x))
expect_error(prob_tox_samples(x, tall = TRUE))
# Expect summary to not error. This is how that is tested, apparently:
expect_error(summary(x), NA)
expect_output(print(x))
expect_true(tibble::is_tibble(as_tibble(x)))
expect_true(nrow(as_tibble(x)) >= num_doses(x))
# Example 3, using tibble
outcomes <- tibble(
cohort = c(1,1,1, 2,2,2),
dose = c(1,1,1, 2,2,2),
tox = c(0,0, 0,0, 1,1)
)
x <- fit(model_fitter, outcomes)
expect_equal(tox_target(x), 0.3)
expect_true(is.numeric(tox_target(x)))
expect_equal(num_patients(x), 6)
expect_true(is.integer(num_patients(x)))
expect_equal(cohort(x), c(1,1,1, 2,2,2))
expect_true(is.integer(cohort(x)))
expect_equal(length(cohort(x)), num_patients(x))
expect_equal(doses_given(x), c(1,1,1, 2,2,2))
expect_true(is.integer(doses_given(x)))
expect_equal(length(doses_given(x)), num_patients(x))
expect_equal(tox(x), c(0,0,0, 0,1,1))
expect_true(is.integer(tox(x)))
expect_equal(length(tox(x)), num_patients(x))
expect_true(all((model_frame(x) - data.frame(patient = c(1,2,3,4,5,6),
cohort = c(1,1,1,2,2,2),
dose = c(1,1,1,2,2,2),
tox = c(0,0,0,0,1,1))) == 0))
expect_equal(nrow(model_frame(x)), num_patients(x))
expect_equal(num_doses(x), 5)
expect_true(is.integer(num_doses(x)))
expect_equal(dose_indices(x), 1:5)
expect_true(is.integer(dose_indices(x)))
expect_equal(length(dose_indices(x)), num_doses(x))
expect_equal(recommended_dose(x), 1)
expect_true(is.integer(recommended_dose(x)))
expect_equal(length(recommended_dose(x)), 1)
expect_equal(continue(x), TRUE)
expect_true(is.logical(continue(x)))
expect_equal(n_at_dose(x), c(3,3,0,0,0))
expect_true(is.integer(n_at_dose(x)))
expect_equal(length(n_at_dose(x)), num_doses(x))
expect_equal(n_at_dose(x, dose = 0), 0)
expect_true(is.integer(n_at_dose(x, dose = 0)))
expect_equal(length(n_at_dose(x, dose = 0)), 1)
expect_equal(n_at_dose(x, dose = 1), 3)
expect_true(is.integer(n_at_dose(x, dose = 1)))
expect_equal(length(n_at_dose(x, dose = 1)), 1)
expect_equal(n_at_dose(x, dose = 'recommended'), 3)
expect_true(is.integer(n_at_dose(x, dose = 'recommended')))
expect_equal(length(n_at_dose(x, dose = 'recommended')), 1)
expect_equal(n_at_recommended_dose(x), 3)
expect_true(is.integer(n_at_recommended_dose(x)))
expect_equal(length(n_at_recommended_dose(x)), 1)
expect_equal(is_randomising(x), FALSE)
expect_true(is.logical(is_randomising(x)))
expect_equal(length(is_randomising(x)), 1)
expect_equal(unname(prob_administer(x)), c(0.5,0.5,0,0,0))
expect_true(is.numeric(prob_administer(x)))
expect_equal(length(prob_administer(x)), num_doses(x))
expect_equal(tox_at_dose(x), c(0,2,0,0,0))
expect_true(is.integer(tox_at_dose(x)))
expect_equal(length(tox_at_dose(x)), num_doses(x))
expect_true(is.numeric(empiric_tox_rate(x)))
expect_equal(length(empiric_tox_rate(x)), num_doses(x))
expect_true(is.numeric(mean_prob_tox(x)))
expect_equal(length(mean_prob_tox(x)), num_doses(x))
expect_true(is.numeric(median_prob_tox(x)))
expect_equal(length(median_prob_tox(x)), num_doses(x))
expect_true(is.logical(dose_admissible(x)))
expect_equal(length(dose_admissible(x)), num_doses(x))
expect_true(is.numeric(prob_tox_quantile(x, p = 0.9)))
expect_equal(length(prob_tox_quantile(x, p = 0.9)), num_doses(x))
expect_true(is.numeric(prob_tox_exceeds(x, 0.5)))
expect_equal(length(prob_tox_exceeds(x, 0.5)), num_doses(x))
expect_true(is.logical(supports_sampling(x)))
expect_error(prob_tox_samples(x))
expect_error(prob_tox_samples(x, tall = TRUE))
# Expect summary to not error. This is how that is tested, apparently:
expect_error(summary(x), NA)
expect_output(print(x))
expect_true(tibble::is_tibble(as_tibble(x)))
expect_true(nrow(as_tibble(x)) >= num_doses(x))
})
test_that('tpi_selector respects suspended doses', {
model <- get_tpi(num_doses = 5, target = 0.3, k1 = 1, k2 = 1.5,
exclusion_certainty = 0.7)
fit <- model %>% fit('2N')
expect_equal(fit %>% recommended_dose(), 3)
expect_true(fit %>% continue())
expect_equal(fit %>% dose_admissible(), rep(TRUE, num_doses(fit)))
fit <- model %>% fit('3TTT')
expect_equal(fit %>% recommended_dose(), 2)
expect_true(fit %>% continue())
expect_equal(fit %>% dose_admissible(), c(TRUE, TRUE, FALSE, FALSE, FALSE))
fit <- model %>% fit('3TTT 2N')
expect_equal(fit %>% recommended_dose(), 2)
expect_true(fit %>% continue())
expect_equal(fit %>% dose_admissible(), c(TRUE, TRUE, FALSE, FALSE, FALSE))
fit <- model %>% fit('3TTT 2N 1N')
expect_equal(fit %>% recommended_dose(), 2)
expect_true(fit %>% continue())
expect_equal(fit %>% dose_admissible(), c(TRUE, TRUE, FALSE, FALSE, FALSE))
fit <- model %>% fit('3TTT 2N 1N 2NNNNNNNNNNNNNNNNNNN')
expect_equal(fit %>% recommended_dose(), 2)
expect_true(fit %>% continue())
expect_equal(fit %>% dose_admissible(), c(TRUE, TRUE, FALSE, FALSE, FALSE))
})
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