test_that('mtpi_selector matches published example.', { # Reproduce decisions conveyed in Figure 2 in Ji et al. (2010) # at https://doi.org/10.1177/1740774510382799 num_doses <- 5 target <- 0.3 model <- get_mtpi(num_doses = num_doses, target = target, epsilon1 = 0.05, epsilon2 = 0.05, 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_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) # Six patients treated fit <- model %>% fit('1NNN 1NNN') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) # Nine patients treated fit <- model %>% fit('1NNN 1NNN 1NNN') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNT 1TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) # Twelve patients treated fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) 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_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NTT 1TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1TTT 1TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) # Thirty patients treated fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1TTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNT 1TTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NTT 1TTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1TTT 1TTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNT 1TTT 1TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NTT 1TTT 1TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1TTT 1TTT 1TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NNT 1TTT 1TTT 1TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1NTT 1TTT 1TTT 1TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NNN 1NNN 1TTT 1TTT 1TTT 1TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NNN 1NNT 1TTT 1TTT 1TTT 1TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NNN 1NTT 1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NNN 1TTT 1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NNT 1TTT 1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1NTT 1TTT 1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNN 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NNT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1NTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNN 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NNT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1NTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNN 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NNT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1NTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNN 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NNT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1NTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT 1TTT') expect_true(is.na(recommended_dose(fit))) expect_false(continue(fit)) expect_output( print(fit), "The model advocates stopping and recommending no dose." ) expect_equal(dose_admissible(fit), rep(FALSE, num_doses(fit))) check_dose_selector_consistency(fit) # Tests at dose 2 ---- # Three patients treated fit <- model %>% fit('2NNN') expect_equal(recommended_dose(fit), 3) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 3." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) # Six patients treated fit <- model %>% fit('2NNN 2NNN') expect_equal(recommended_dose(fit), 3) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 3." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNT') expect_equal(recommended_dose(fit), 3) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 3." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2TTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) # Nine patients treated fit <- model %>% fit('2NNN 2NNN 2NNN') expect_equal(recommended_dose(fit), 3) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 3." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNT') expect_equal(recommended_dose(fit), 3) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 3." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2TTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNT 2TTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) # Twelve patients treated fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN') expect_equal(recommended_dose(fit), 3) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 3." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNT') expect_equal(recommended_dose(fit), 3) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 3." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NTT') expect_equal(recommended_dose(fit), 3) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 3." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2TTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNT 2TTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NTT 2TTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) # Thirty patients treated fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN') expect_equal(recommended_dose(fit), 3) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 3." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNT') expect_equal(recommended_dose(fit), 3) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 3." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NTT') expect_equal(recommended_dose(fit), 3) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 3." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2TTT') expect_equal(recommended_dose(fit), 3) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 3." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNT 2TTT') expect_equal(recommended_dose(fit), 3) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 3." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NTT 2TTT') expect_equal(recommended_dose(fit), 3) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 3." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2TTT 2TTT') expect_equal(recommended_dose(fit), 3) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 3." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNT 2TTT 2TTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NNT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2NTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NNN 2NNN 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NNN 2NNT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 2) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NNN 2NTT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NNN 2TTT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NNT 2TTT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2NTT 2TTT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNN 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NNT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2NTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNN 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NNT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2NTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNN 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NNT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2NTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNN 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NNT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2NTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT 2TTT') expect_equal(recommended_dose(fit), 1) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 1." ) expect_equal(dose_admissible(fit), c(TRUE, FALSE, FALSE, FALSE, FALSE)) check_dose_selector_consistency(fit) # 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_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) # Six patients treated fit <- model %>% fit('5NNN 5NNN') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5TTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) # Nine patients treated fit <- model %>% fit('5NNN 5NNN 5NNN') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5TTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNT 5TTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) # Twelve patients treated fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5TTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNT 5TTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NTT 5TTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) # Thirty patients treated fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5TTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNT 5TTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NTT 5TTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5TTT 5TTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNT 5TTT 5TTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NNT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5NTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NNN 5NNN 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NNN 5NNT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 5) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 5." ) expect_equal(dose_admissible(fit), rep(TRUE, num_doses(fit))) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NNN 5NTT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NNN 5TTT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NNT 5TTT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5NTT 5TTT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNN 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NNT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5NTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNN 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NNT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5NTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNN 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NNT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5NTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNN 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NNT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5NTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) fit <- model %>% fit('5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT 5TTT') expect_equal(recommended_dose(fit), 4) expect_true(continue(fit)) expect_output( print(fit), "The model advocates continuing at dose 4." ) expect_equal(dose_admissible(fit), c(TRUE, TRUE, TRUE, TRUE, FALSE)) check_dose_selector_consistency(fit) }) test_that('mtpi_selector supports correct interface.', { num_doses <- 5 target <- 0.3 model_fitter <- get_mtpi(num_doses = num_doses, target = target, epsilon1 = 0.05, epsilon2 = 0.05, 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(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(is_randomising(x), FALSE) expect_true(is.logical(is_randomising(x))) expect_equal(length(is_randomising(x)), 1) 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('mtpi_selector respects suspended doses', { model <- get_mtpi(num_doses = 5, target = 0.3, epsilon1 = 0.05, epsilon2 = 0.05, exclusion_certainty = 0.7) fit <- model %>% fit('2N') expect_equal(fit %>% recommended_dose(), 3) expect_true(fit %>% continue()) expect_output( print(fit), "The model advocates continuing at dose 3." ) 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_output( print(fit), "The model advocates continuing at dose 2." ) 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_output( print(fit), "The model advocates continuing at dose 2." ) 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_output( print(fit), "The model advocates continuing at dose 2." ) 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_output( print(fit), "The model advocates continuing at dose 2." ) expect_equal(fit %>% dose_admissible(), c(TRUE, TRUE, FALSE, FALSE, FALSE)) })