tests/testthat/test_boin12.R
In brockk/dosefinding: A Modular Approach to Dose-Finding Clinical Trials
test_that('BOIN12 matches published example.', {
model <- get_boin12(num_doses = 5, phi_t = 0.35, phi_e = 0.25,
u2 = 40, u3 = 60, n_star = 6) %>%
stop_at_n(n = 30) %>%
stop_when_n_at_dose(n = 12, dose = "any")
# p.1396 of Lin et al.
fit <- model %>% fit("1NNN 2ENT 3ETT 2EEN")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
check_dose_selector_consistency(fit)
# Section 6 and Figure S2 of Data Supplement
fit <- model %>% fit("1NNN")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB")
expect_equal(recommended_dose(fit), 3)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 3."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB 3NEE")
expect_equal(recommended_dose(fit), 3)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 3."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB 3NEE 3NTN")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB 3NEE 3NTN 4ETE")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB 3NEE 3NTN 4ETE 4NBE")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB 3NEE 3NTN 4ETE 4NBE 4BNN")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB 3NEE 3NTN 4ETE 4NBE 4BNN 5BEN")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB 3NEE 3NTN 4ETE 4NBE 4BNN 5BEN 5NBT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB 3NEE 3NTN 4ETE 4NBE 4BNN 5BEN 5NBT 4NEN")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), FALSE)
expect_output(
print(fit),
"The model advocates stopping and recommending dose 4."
)
check_dose_selector_consistency(fit)
})
test_that('BOIN12 matches MDAnderson Shiny app - parameterisation 1', {
# See https://biostatistics.mdanderson.org/shinyapps/BOIN12/
# Default parameterisation
model <- get_boin12(num_doses = 5, phi_t = 0.35, phi_e = 0.25,
u1 = 100, u2 = 40, u3 = 60, u4 = 0,
n_star = 6, c_t = 0.95, c_e = 0.9,
start_dose = 1, prior_alpha = 1, prior_beta = 1) %>%
stop_at_n(n = 36) %>%
stop_when_n_at_dose(n = 12, dose = "any")
# Starting at bottom dose
# Breaks the app
# fit <- model %>% fit("1BBB")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
fit <- model %>% fit("1EBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1EEB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1EEE")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1EET")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1ETB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1ETT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NEB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NEE")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NET")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("1NNB")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("1NNE")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("1NNN")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("1NNT")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("1NTB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NTT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
# Breaks the app
# fit <- model %>% fit("1TBB")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
# Breaks the app
# fit <- model %>% fit("1TTB")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
# Breaks the app
# fit <- model %>% fit("1TTT")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
# Starting at middling dose
fit <- model %>% fit("2BBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2EBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2EEB")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("2EEE")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("2EET")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("2ETB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2ETT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NEB")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("2NEE")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("2NET")
expect_equal(recommended_dose(fit), 3)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 3."
)
fit <- model %>% fit("2NNB")
expect_equal(recommended_dose(fit), 3)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 3."
)
fit <- model %>% fit("2NNE")
expect_equal(recommended_dose(fit), 3)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 3."
)
fit <- model %>% fit("2NNN")
expect_equal(recommended_dose(fit), 3)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 3."
)
fit <- model %>% fit("2NNT")
expect_equal(recommended_dose(fit), 3)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 3."
)
fit <- model %>% fit("2NTB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NTT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2TBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2TTB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2TTT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
# Starting at top dose
fit <- model %>% fit("5BBB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5EBB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5EEB")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
fit <- model %>% fit("5EEE")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
fit <- model %>% fit("5EET")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
fit <- model %>% fit("5ETB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5ETT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NBB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NEB")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
fit <- model %>% fit("5NEE")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
fit <- model %>% fit("5NET")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NNB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NNE")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NNN")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NNT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NTB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NTT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5TBB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5TTB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5TTT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
})
test_that('BOIN12 matches MDAnderson Shiny app - parameterisation 2', {
# See https://biostatistics.mdanderson.org/shinyapps/BOIN12/
# Non-standard parameterisation
model <- get_boin12(num_doses = 5, phi_t = 0.15, phi_e = 0.4,
u1 = 100, u2 = 50, u3 = 30, u4 = 0,
n_star = 6, c_t = 0.9, c_e = 0.8,
start_dose = 1, prior_alpha = 1, prior_beta = 1) %>%
stop_at_n(n = 36) %>%
stop_when_n_at_dose(n = 12, dose = "any")
# Starting at bottom dose
# Breaks the app
# fit <- model %>% fit("1BBB")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
fit <- model %>% fit("1EBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1EEB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1EEE")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1EET")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1ETB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1ETT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NEB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NEE")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NET")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NNB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NNE")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("1NNN")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
# Breaks the app
# fit <- model %>% fit("1NNT")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
fit <- model %>% fit("1NTB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
# Breaks the app
# fit <- model %>% fit("1NTT")
# expect_equal(recommended_dose(fit), 1)
# expect_equal(continue(fit), TRUE)
# Breaks the app
# fit <- model %>% fit("1TBB")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
# Breaks the app
# fit <- model %>% fit("1TTB")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
# Breaks the app
# fit <- model %>% fit("1TTT")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
# Starting at middling dose
fit <- model %>% fit("2BBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2EBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2EEB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2EEE")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("2EET")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2ETB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2ETT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NEB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NEE")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("2NET")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NNB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
# fit <- model %>% fit("2NNE")
# expect_equal(recommended_dose(fit), 1)
# expect_equal(continue(fit), TRUE)
# In this sitation, d1 and d3 have equal utility. Their Shiny app chooses d1.
# In other situations, their app will resolve ties by selelcting the higher
# dose. This remains an ambiguous situation.
fit <- model %>% fit("2NNN")
expect_equal(recommended_dose(fit), 3)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 3."
)
fit <- model %>% fit("2NNT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NTB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NTT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2TBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2TTB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2TTT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
# Starting at top dose
fit <- model %>% fit("5BBB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5EBB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5EEB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5EEE")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
fit <- model %>% fit("5EET")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5ETB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5ETT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NBB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NEB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NEE")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
fit <- model %>% fit("5NET")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NNB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NNE")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NNN")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NNT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NTB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NTT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5TBB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5TTB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5TTT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
})
test_that('boin12_selector supports correct interface.', {
model_fitter <- get_boin12(num_doses = 5, phi_t = 0.35, phi_e = 0.25,
u2 = 40, u3 = 60, n_star = 6) %>%
stop_at_n(n = 30) %>%
stop_when_n_at_dose(n = 12, dose = "any")
# Example 1, using outcome string
x <- fit(model_fitter, '1NEN 2NBT')
expect_true(is.null(tox_target(x)))
expect_equal(tox_limit(x), 0.35)
expect_true(is.numeric(tox_limit(x)))
expect_equal(eff_limit(x), 0.25)
expect_true(is.numeric(eff_limit(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), unname(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(is.numeric(weight(x)))
expect_equal(length(weight(x)), num_patients(x))
expect_equal(num_tox(x), 2)
expect_true(is.integer(num_tox(x)))
expect_equal(eff(x), c(0,1,0, 0,1,0))
expect_true(is.integer(eff(x)))
expect_equal(length(eff(x)), num_patients(x))
expect_equal(num_eff(x), 2)
expect_true(is.integer(num_eff(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),
eff = c(0,1,0,0,1,0))) == 0))
expect_equal(nrow(model_frame(x)), num_patients(x))
expect_equal(num_doses(x), 5)
expect_true(is.integer(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))
expect_true(is.integer(recommended_dose(x)))
expect_equal(length(recommended_dose(x)), 1)
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_true(is.integer(n_at_dose(x, dose = 'recommended')))
expect_equal(length(n_at_dose(x, dose = 'recommended')), 1)
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_equal(eff_at_dose(x), c(1,1,0,0,0))
expect_true(is.integer(eff_at_dose(x)))
expect_equal(length(eff_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.numeric(empiric_eff_rate(x)))
expect_equal(length(empiric_eff_rate(x)), num_doses(x))
expect_true(is.numeric(mean_prob_eff(x)))
expect_equal(length(mean_prob_eff(x)), num_doses(x))
expect_true(is.numeric(median_prob_eff(x)))
expect_equal(length(median_prob_eff(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.numeric(prob_eff_quantile(x, p = 0.9)))
expect_equal(length(prob_eff_quantile(x, p = 0.9)), num_doses(x))
expect_true(is.numeric(prob_eff_exceeds(x, 0.5)))
expect_equal(length(prob_eff_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_error(prob_eff_samples(x))
expect_error(prob_eff_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_true(is.null(tox_target(x)))
expect_equal(tox_limit(x), 0.35)
expect_true(is.numeric(tox_limit(x)))
expect_equal(eff_limit(x), 0.25)
expect_true(is.numeric(eff_limit(x)))
expect_equal(num_patients(x), 0)
expect_true(is.integer(num_patients(x)))
expect_equal(cohort(x), integer(length = 0))
expect_true(is.integer(cohort(x)))
expect_equal(length(cohort(x)), num_patients(x))
expect_equal(doses_given(x), integer(length = 0))
expect_true(is.integer(doses_given(x)))
expect_equal(length(doses_given(x)), num_patients(x))
expect_equal(tox(x), integer(length = 0))
expect_true(is.integer(tox(x)))
expect_equal(length(tox(x)), num_patients(x))
expect_true(is.numeric(weight(x)))
expect_equal(length(weight(x)), num_patients(x))
expect_equal(num_tox(x), 0)
expect_true(is.integer(num_tox(x)))
expect_equal(eff(x), integer(length = 0))
expect_true(is.integer(eff(x)))
expect_equal(length(eff(x)), num_patients(x))
expect_equal(num_eff(x), 0)
expect_true(is.integer(num_eff(x)))
mf <- model_frame(x)
expect_equal(nrow(mf), 0)
expect_equal(ncol(mf), 5)
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(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_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_equal(eff_at_dose(x), c(0,0,0,0,0))
expect_true(is.integer(eff_at_dose(x)))
expect_equal(length(eff_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.numeric(empiric_eff_rate(x)))
expect_equal(length(empiric_eff_rate(x)), num_doses(x))
expect_true(is.numeric(mean_prob_eff(x)))
expect_equal(length(mean_prob_eff(x)), num_doses(x))
expect_true(is.numeric(median_prob_eff(x)))
expect_equal(length(median_prob_eff(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.numeric(prob_eff_quantile(x, p = 0.9)))
expect_equal(length(prob_eff_quantile(x, p = 0.9)), num_doses(x))
expect_true(is.numeric(prob_eff_exceeds(x, 0.5)))
expect_equal(length(prob_eff_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_error(prob_eff_samples(x))
expect_error(prob_eff_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 of outcomes
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),
eff = c(0,1, 0,0, 1,0)
)
x <- fit(model_fitter, outcomes)
expect_true(is.null(tox_target(x)))
expect_equal(tox_limit(x), 0.35)
expect_true(is.numeric(tox_limit(x)))
expect_equal(eff_limit(x), 0.25)
expect_true(is.numeric(eff_limit(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), unname(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(is.numeric(weight(x)))
expect_equal(length(weight(x)), num_patients(x))
expect_equal(num_tox(x), 2)
expect_true(is.integer(num_tox(x)))
expect_equal(eff(x), c(0,1,0, 0,1,0))
expect_true(is.integer(eff(x)))
expect_equal(length(eff(x)), num_patients(x))
expect_equal(num_eff(x), 2)
expect_true(is.integer(num_eff(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),
eff = c(0,1,0,0,1,0))) == 0))
expect_equal(nrow(model_frame(x)), num_patients(x))
expect_equal(num_doses(x), 5)
expect_true(is.integer(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))
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_true(is.integer(n_at_dose(x, dose = 'recommended')))
expect_equal(length(n_at_dose(x, dose = 'recommended')), 1)
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_equal(eff_at_dose(x), c(1,1,0,0,0))
expect_true(is.integer(eff_at_dose(x)))
expect_equal(length(eff_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.numeric(empiric_eff_rate(x)))
expect_equal(length(empiric_eff_rate(x)), num_doses(x))
expect_true(is.numeric(mean_prob_eff(x)))
expect_equal(length(mean_prob_eff(x)), num_doses(x))
expect_true(is.numeric(median_prob_eff(x)))
expect_equal(length(median_prob_eff(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.numeric(prob_eff_quantile(x, p = 0.9)))
expect_equal(length(prob_eff_quantile(x, p = 0.9)), num_doses(x))
expect_true(is.numeric(prob_eff_exceeds(x, 0.5)))
expect_equal(length(prob_eff_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_error(prob_eff_samples(x))
expect_error(prob_eff_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))
})
brockk/dosefinding documentation built on April 5, 2025, 5:53 p.m.
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test_that('BOIN12 matches published example.', {
model <- get_boin12(num_doses = 5, phi_t = 0.35, phi_e = 0.25,
u2 = 40, u3 = 60, n_star = 6) %>%
stop_at_n(n = 30) %>%
stop_when_n_at_dose(n = 12, dose = "any")
# p.1396 of Lin et al.
fit <- model %>% fit("1NNN 2ENT 3ETT 2EEN")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
check_dose_selector_consistency(fit)
# Section 6 and Figure S2 of Data Supplement
fit <- model %>% fit("1NNN")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB")
expect_equal(recommended_dose(fit), 3)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 3."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB 3NEE")
expect_equal(recommended_dose(fit), 3)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 3."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB 3NEE 3NTN")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB 3NEE 3NTN 4ETE")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB 3NEE 3NTN 4ETE 4NBE")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB 3NEE 3NTN 4ETE 4NBE 4BNN")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB 3NEE 3NTN 4ETE 4NBE 4BNN 5BEN")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB 3NEE 3NTN 4ETE 4NBE 4BNN 5BEN 5NBT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
check_dose_selector_consistency(fit)
fit <- model %>% fit("1NNN 2NNB 3NEE 3NTN 4ETE 4NBE 4BNN 5BEN 5NBT 4NEN")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), FALSE)
expect_output(
print(fit),
"The model advocates stopping and recommending dose 4."
)
check_dose_selector_consistency(fit)
})
test_that('BOIN12 matches MDAnderson Shiny app - parameterisation 1', {
# See https://biostatistics.mdanderson.org/shinyapps/BOIN12/
# Default parameterisation
model <- get_boin12(num_doses = 5, phi_t = 0.35, phi_e = 0.25,
u1 = 100, u2 = 40, u3 = 60, u4 = 0,
n_star = 6, c_t = 0.95, c_e = 0.9,
start_dose = 1, prior_alpha = 1, prior_beta = 1) %>%
stop_at_n(n = 36) %>%
stop_when_n_at_dose(n = 12, dose = "any")
# Starting at bottom dose
# Breaks the app
# fit <- model %>% fit("1BBB")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
fit <- model %>% fit("1EBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1EEB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1EEE")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1EET")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1ETB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1ETT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NEB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NEE")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NET")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("1NNB")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("1NNE")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("1NNN")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("1NNT")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("1NTB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NTT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
# Breaks the app
# fit <- model %>% fit("1TBB")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
# Breaks the app
# fit <- model %>% fit("1TTB")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
# Breaks the app
# fit <- model %>% fit("1TTT")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
# Starting at middling dose
fit <- model %>% fit("2BBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2EBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2EEB")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("2EEE")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("2EET")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("2ETB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2ETT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NEB")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("2NEE")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("2NET")
expect_equal(recommended_dose(fit), 3)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 3."
)
fit <- model %>% fit("2NNB")
expect_equal(recommended_dose(fit), 3)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 3."
)
fit <- model %>% fit("2NNE")
expect_equal(recommended_dose(fit), 3)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 3."
)
fit <- model %>% fit("2NNN")
expect_equal(recommended_dose(fit), 3)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 3."
)
fit <- model %>% fit("2NNT")
expect_equal(recommended_dose(fit), 3)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 3."
)
fit <- model %>% fit("2NTB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NTT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2TBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2TTB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2TTT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
# Starting at top dose
fit <- model %>% fit("5BBB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5EBB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5EEB")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
fit <- model %>% fit("5EEE")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
fit <- model %>% fit("5EET")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
fit <- model %>% fit("5ETB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5ETT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NBB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NEB")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
fit <- model %>% fit("5NEE")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
fit <- model %>% fit("5NET")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NNB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NNE")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NNN")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NNT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NTB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NTT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5TBB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5TTB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5TTT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
})
test_that('BOIN12 matches MDAnderson Shiny app - parameterisation 2', {
# See https://biostatistics.mdanderson.org/shinyapps/BOIN12/
# Non-standard parameterisation
model <- get_boin12(num_doses = 5, phi_t = 0.15, phi_e = 0.4,
u1 = 100, u2 = 50, u3 = 30, u4 = 0,
n_star = 6, c_t = 0.9, c_e = 0.8,
start_dose = 1, prior_alpha = 1, prior_beta = 1) %>%
stop_at_n(n = 36) %>%
stop_when_n_at_dose(n = 12, dose = "any")
# Starting at bottom dose
# Breaks the app
# fit <- model %>% fit("1BBB")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
fit <- model %>% fit("1EBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1EEB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1EEE")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1EET")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1ETB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1ETT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NEB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NEE")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NET")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NNB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("1NNE")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("1NNN")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
# Breaks the app
# fit <- model %>% fit("1NNT")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
fit <- model %>% fit("1NTB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
# Breaks the app
# fit <- model %>% fit("1NTT")
# expect_equal(recommended_dose(fit), 1)
# expect_equal(continue(fit), TRUE)
# Breaks the app
# fit <- model %>% fit("1TBB")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
# Breaks the app
# fit <- model %>% fit("1TTB")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
# Breaks the app
# fit <- model %>% fit("1TTT")
# expect_equal(recommended_dose(fit), 2)
# expect_equal(continue(fit), TRUE)
# Starting at middling dose
fit <- model %>% fit("2BBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2EBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2EEB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2EEE")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("2EET")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2ETB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2ETT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NEB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NEE")
expect_equal(recommended_dose(fit), 2)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 2."
)
fit <- model %>% fit("2NET")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NNB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
# fit <- model %>% fit("2NNE")
# expect_equal(recommended_dose(fit), 1)
# expect_equal(continue(fit), TRUE)
# In this sitation, d1 and d3 have equal utility. Their Shiny app chooses d1.
# In other situations, their app will resolve ties by selelcting the higher
# dose. This remains an ambiguous situation.
fit <- model %>% fit("2NNN")
expect_equal(recommended_dose(fit), 3)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 3."
)
fit <- model %>% fit("2NNT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NTB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2NTT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2TBB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2TTB")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
fit <- model %>% fit("2TTT")
expect_equal(recommended_dose(fit), 1)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 1."
)
# Starting at top dose
fit <- model %>% fit("5BBB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5EBB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5EEB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5EEE")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
fit <- model %>% fit("5EET")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5ETB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5ETT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NBB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NEB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NEE")
expect_equal(recommended_dose(fit), 5)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 5."
)
fit <- model %>% fit("5NET")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NNB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NNE")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NNN")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NNT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NTB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5NTT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5TBB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5TTB")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
fit <- model %>% fit("5TTT")
expect_equal(recommended_dose(fit), 4)
expect_equal(continue(fit), TRUE)
expect_output(
print(fit),
"The model advocates continuing at dose 4."
)
})
test_that('boin12_selector supports correct interface.', {
model_fitter <- get_boin12(num_doses = 5, phi_t = 0.35, phi_e = 0.25,
u2 = 40, u3 = 60, n_star = 6) %>%
stop_at_n(n = 30) %>%
stop_when_n_at_dose(n = 12, dose = "any")
# Example 1, using outcome string
x <- fit(model_fitter, '1NEN 2NBT')
expect_true(is.null(tox_target(x)))
expect_equal(tox_limit(x), 0.35)
expect_true(is.numeric(tox_limit(x)))
expect_equal(eff_limit(x), 0.25)
expect_true(is.numeric(eff_limit(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), unname(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(is.numeric(weight(x)))
expect_equal(length(weight(x)), num_patients(x))
expect_equal(num_tox(x), 2)
expect_true(is.integer(num_tox(x)))
expect_equal(eff(x), c(0,1,0, 0,1,0))
expect_true(is.integer(eff(x)))
expect_equal(length(eff(x)), num_patients(x))
expect_equal(num_eff(x), 2)
expect_true(is.integer(num_eff(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),
eff = c(0,1,0,0,1,0))) == 0))
expect_equal(nrow(model_frame(x)), num_patients(x))
expect_equal(num_doses(x), 5)
expect_true(is.integer(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))
expect_true(is.integer(recommended_dose(x)))
expect_equal(length(recommended_dose(x)), 1)
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_true(is.integer(n_at_dose(x, dose = 'recommended')))
expect_equal(length(n_at_dose(x, dose = 'recommended')), 1)
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_equal(eff_at_dose(x), c(1,1,0,0,0))
expect_true(is.integer(eff_at_dose(x)))
expect_equal(length(eff_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.numeric(empiric_eff_rate(x)))
expect_equal(length(empiric_eff_rate(x)), num_doses(x))
expect_true(is.numeric(mean_prob_eff(x)))
expect_equal(length(mean_prob_eff(x)), num_doses(x))
expect_true(is.numeric(median_prob_eff(x)))
expect_equal(length(median_prob_eff(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.numeric(prob_eff_quantile(x, p = 0.9)))
expect_equal(length(prob_eff_quantile(x, p = 0.9)), num_doses(x))
expect_true(is.numeric(prob_eff_exceeds(x, 0.5)))
expect_equal(length(prob_eff_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_error(prob_eff_samples(x))
expect_error(prob_eff_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_true(is.null(tox_target(x)))
expect_equal(tox_limit(x), 0.35)
expect_true(is.numeric(tox_limit(x)))
expect_equal(eff_limit(x), 0.25)
expect_true(is.numeric(eff_limit(x)))
expect_equal(num_patients(x), 0)
expect_true(is.integer(num_patients(x)))
expect_equal(cohort(x), integer(length = 0))
expect_true(is.integer(cohort(x)))
expect_equal(length(cohort(x)), num_patients(x))
expect_equal(doses_given(x), integer(length = 0))
expect_true(is.integer(doses_given(x)))
expect_equal(length(doses_given(x)), num_patients(x))
expect_equal(tox(x), integer(length = 0))
expect_true(is.integer(tox(x)))
expect_equal(length(tox(x)), num_patients(x))
expect_true(is.numeric(weight(x)))
expect_equal(length(weight(x)), num_patients(x))
expect_equal(num_tox(x), 0)
expect_true(is.integer(num_tox(x)))
expect_equal(eff(x), integer(length = 0))
expect_true(is.integer(eff(x)))
expect_equal(length(eff(x)), num_patients(x))
expect_equal(num_eff(x), 0)
expect_true(is.integer(num_eff(x)))
mf <- model_frame(x)
expect_equal(nrow(mf), 0)
expect_equal(ncol(mf), 5)
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(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_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_equal(eff_at_dose(x), c(0,0,0,0,0))
expect_true(is.integer(eff_at_dose(x)))
expect_equal(length(eff_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.numeric(empiric_eff_rate(x)))
expect_equal(length(empiric_eff_rate(x)), num_doses(x))
expect_true(is.numeric(mean_prob_eff(x)))
expect_equal(length(mean_prob_eff(x)), num_doses(x))
expect_true(is.numeric(median_prob_eff(x)))
expect_equal(length(median_prob_eff(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.numeric(prob_eff_quantile(x, p = 0.9)))
expect_equal(length(prob_eff_quantile(x, p = 0.9)), num_doses(x))
expect_true(is.numeric(prob_eff_exceeds(x, 0.5)))
expect_equal(length(prob_eff_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_error(prob_eff_samples(x))
expect_error(prob_eff_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 of outcomes
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),
eff = c(0,1, 0,0, 1,0)
)
x <- fit(model_fitter, outcomes)
expect_true(is.null(tox_target(x)))
expect_equal(tox_limit(x), 0.35)
expect_true(is.numeric(tox_limit(x)))
expect_equal(eff_limit(x), 0.25)
expect_true(is.numeric(eff_limit(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), unname(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(is.numeric(weight(x)))
expect_equal(length(weight(x)), num_patients(x))
expect_equal(num_tox(x), 2)
expect_true(is.integer(num_tox(x)))
expect_equal(eff(x), c(0,1,0, 0,1,0))
expect_true(is.integer(eff(x)))
expect_equal(length(eff(x)), num_patients(x))
expect_equal(num_eff(x), 2)
expect_true(is.integer(num_eff(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),
eff = c(0,1,0,0,1,0))) == 0))
expect_equal(nrow(model_frame(x)), num_patients(x))
expect_equal(num_doses(x), 5)
expect_true(is.integer(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))
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_true(is.integer(n_at_dose(x, dose = 'recommended')))
expect_equal(length(n_at_dose(x, dose = 'recommended')), 1)
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_equal(eff_at_dose(x), c(1,1,0,0,0))
expect_true(is.integer(eff_at_dose(x)))
expect_equal(length(eff_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.numeric(empiric_eff_rate(x)))
expect_equal(length(empiric_eff_rate(x)), num_doses(x))
expect_true(is.numeric(mean_prob_eff(x)))
expect_equal(length(mean_prob_eff(x)), num_doses(x))
expect_true(is.numeric(median_prob_eff(x)))
expect_equal(length(median_prob_eff(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.numeric(prob_eff_quantile(x, p = 0.9)))
expect_equal(length(prob_eff_quantile(x, p = 0.9)), num_doses(x))
expect_true(is.numeric(prob_eff_exceeds(x, 0.5)))
expect_equal(length(prob_eff_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_error(prob_eff_samples(x))
expect_error(prob_eff_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))
})
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