Nothing
TOLERANCE <- 1e-2
test_that("Table #2: POLARIX ", {
# OS monitoring guideline retrospectively applied to Motivating Example 1 with δnull = 1.3, δalt = 0.80, γFA = 0.025 and βPA = 0.10.
res <- bounds(
events = c(60, 89, 110, 131, 178),
power_int = 0.9,
falsepos = 0.025,
hr_null = 1.3,
hr_alt = 0.8
)
# check for errors in the provided results.
expect_equal(
as.numeric(res$summary$"OS HR threshold for positivity"),
# OS HR threshold for positivity
c(1.114, 1.050, 1.021, 1.001, 0.969),
tolerance = TOLERANCE
)
expect_equal(
as.numeric(res$summary$"One-sided false positive error rate"),
# One-sided false positive error rate
c(0.275, 0.157, 0.103, 0.067, 0.025),
tolerance = TOLERANCE
)
expect_equal(as.numeric(res$summary$"Level of 2-sided CI needed to rule out delta null"),
# Level of 2-sided CI needed to rule out
c(45, 69, 79, 87, 95),
tolerance = 1e-1
)
expect_equal(as.numeric(res$summary$"Probability of meeting positivity threshold under delta alt"),
# Probability of meeting positivity threshold under δalt
c(0.90, 0.90, 0.90, 0.90, 0.90),
tolerance = TOLERANCE
)
})
test_that("Table#3: Intermediate events", {
# OS monitoring guideline with δnull = 1.3, δalt = 0.70, γFA = 0.10 and βPA = 0.10.
res <- bounds(
events = c(28, 42, 70),
power_int = 0.9,
falsepos = 0.1,
hr_null = 1.3,
hr_alt = 0.7,
hr_marg_benefit = 0.95
)
# check for errors in the provided results.
expect_equal(as.numeric(res$summary$"OS HR threshold for positivity"),
# OS HR threshold for positivity
c(1.136, 1.040, 0.957),
tolerance = TOLERANCE
)
expect_equal(as.numeric(res$summary$"One-sided false positive error rate"),
# One-sided false positive error rate
c(0.36, 0.23, 0.1),
tolerance = TOLERANCE
)
expect_equal(as.numeric(res$summary$"Level of 2-sided CI needed to rule out delta null"),
# Level of 2-sided CI needed to rule out
c(28, 53, 80),
tolerance = 1e-1
)
expect_equal(as.numeric(res$summary$"Probability of meeting positivity threshold under delta alt"),
# Probability of meeting positivity threshold under δalt
c(0.9, 0.9, 0.905),
tolerance = TOLERANCE
)
expect_equal(as.numeric(res$summary$"Probability of meeting positivity threshold under incremental benefit"),
# Probability of meeting positivity threshold under HR = 0.95
c(0.682, 0.615, 0.512),
tolerance = TOLERANCE
)
})
test_that("Table#4: Example 2", {
# OS monitoring guideline with δnull = 1.3, δalt = 0.95, γFA = 0.2 and βPA = 0.25.
res <- bounds(
events = c(28, 42, 70),
power_int = 0.75,
falsepos = 0.2,
hr_null = 1.3,
hr_alt = 0.95,
hr_marg_benefit = 1
)
# check for errors in the provided results.
expect_equal(as.numeric(res$summary$"OS HR threshold for positivity"),
# OS HR threshold for positivity
c(1.226, 1.170, 1.063),
tolerance = TOLERANCE
)
expect_equal(as.numeric(res$summary$"One-sided false positive error rate"),
# One-sided false positive error rate
c(0.438, 0.366, 0.2),
tolerance = TOLERANCE
)
expect_equal(as.numeric(res$summary$"Level of 2-sided CI needed to rule out delta null"),
# Level of 2-sided CI needed to rule out
c(12, 27, 60),
tolerance = 5e-1
)
expect_equal(as.numeric(res$summary$"Probability of meeting positivity threshold under delta alt"),
# Probability of meeting positivity threshold under δalt
c(0.750, 0.750, 0.681),
tolerance = TOLERANCE
)
expect_equal(as.numeric(res$summary$"Probability of meeting positivity threshold under incremental benefit"),
# Probability of meeting positivity threshold under HR = 1
c(0.705, 0.694, 0.601),
tolerance = TOLERANCE
)
})
test_that("Table#5: Example 2", {
# OS monitoring guideline applied to Motivating Example 2 with δnull = 1.333, δalt = 0.7, γFA = 0.20 and βPA = 0.1.
res <- bounds(
events = c(22, 34),
power_int = 0.9,
falsepos = 0.20,
hr_null = 4 / 3,
hr_alt = 0.7,
hr_marg_benefit = 0.95
)
# check for errors in the provided results.
expect_equal(as.numeric(res$summary$"OS HR threshold for positivity"),
# OS HR threshold for positivity
c(1.209, 0.999),
tolerance = TOLERANCE
)
expect_equal(as.numeric(res$summary$"One-sided false positive error rate"),
# One-sided false positive error rate
c(0.409, 0.2),
tolerance = TOLERANCE
)
expect_equal(as.numeric(res$summary$"Level of 2-sided CI needed to rule out delta null"),
# Level of 2-sided CI needed to rule out
c(18, 60),
tolerance = 1e-1
)
expect_equal(as.numeric(res$summary$"Probability of meeting positivity threshold under delta alt"), # Probability of meeting positivity threshold under δalt
c(0.9, 0.85),
tolerance = TOLERANCE
)
expect_equal(as.numeric(res$summary$"Probability of meeting positivity threshold under incremental benefit"),
# Probability of meeting positivity threshold under HR = 0.95
c(0.714, 0.558),
tolerance = TOLERANCE
)
})
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