Nothing
# Set a tolerance for numeric comparisons
tol <- .Machine$double.eps ^ 0.5
################################################################################
# Standard negatives
test_that("Typical results for negatives are returned as negatives", {
# Low
expect_that(qft.criteria.070(data.frame(nil = 0.01,
tb = 0.01,
mito = 10)),
matches("Negative")
)
# Borderline
expect_that(qft.criteria.070(data.frame(nil = 0.01,
tb = 0.70,
mito = 10)),
matches("Negative")
)
# Slightly higher
expect_that(qft.criteria.070(data.frame(nil = 0.50,
tb = 1.19,
mito = 10)),
matches("Negative")
)
# High, but tb - nil < .25*nil
expect_that(qft.criteria.070(data.frame(nil = 4.00,
tb = 4.99,
mito = 10)),
matches("Negative")
)
# Nil can be higher than TB
expect_that(qft.criteria.070(data.frame(nil = 0.70,
tb = 0.01,
mito = 10)),
matches("Negative")
)
# Close to mitogen-indeterminate threshold
expect_that(qft.criteria.070(data.frame(nil = 0.01,
tb = 0.01,
mito = 0.51)),
matches("Negative")
)
})
################################################################################
# Standard positives
test_that("Typical results for positives are returned as positives", {
# Borderline
expect_that(qft.criteria.070(data.frame(nil = 0.01,
tb = 0.71,
mito = 10)),
matches("Positive")
)
# Slightly higher
expect_that(qft.criteria.070(data.frame(nil = 0.50,
tb = 1.20,
mito = 10)),
matches("Positive")
)
# High, tb - nil just over .25*nil
expect_that(qft.criteria.070(data.frame(nil = 4.00,
tb = 5.00,
mito = 10)),
matches("Positive")
)
# Even if mito - nil < 0.50
expect_that(qft.criteria.070(data.frame(nil = 4.00,
tb = 5.00,
mito = 4.25)),
matches("Positive")
)
})
################################################################################
# Indeterminate - high nil
test_that("Typical results for high-nil indeterminates are returned as high-nil indeterminates", {
# Nil over 8, everything else standard
expect_that(qft.criteria.070(data.frame(nil = 8.01,
tb = 0.01,
mito = 10)),
matches("Indeterminate - high nil")
)
# Would be positive if nil weren't over 8
expect_that(qft.criteria.070(data.frame(nil = 8.01,
tb = 11.00,
mito = 10)),
matches("Indeterminate - high nil")
)
})
################################################################################
# Indeterminate - nil too close to mito
test_that("Typical results for mito~nil indeterminates are returned as mito~nil indeterminates", {
# Lower range
expect_that(qft.criteria.070(data.frame(nil = 0.01,
tb = 0.01,
mito = 0.50)),
matches("Indeterminate - mitogen too close to nil")
)
# Higher range
expect_that(qft.criteria.070(data.frame(nil = 0.50,
tb = 0.70,
mito = 0.99)),
matches("Indeterminate - mitogen too close to nil")
)
# Higher still
expect_that(qft.criteria.070(data.frame(nil = 5.00,
tb = 4.00,
mito = 5.25)),
matches("Indeterminate - mitogen too close to nil")
)
})
################################################################################
# Numeric comparison tolerance checks
test_that("Results are correct in the presence of floating point comparison uncertainty", {
# Nil ~ 8.00
expect_that(qft.criteria.070(data.frame(nil = 8.01,
tb = 0.01,
mito = 10)),
matches("Indeterminate - high nil")
)
expect_that(qft.criteria.070(data.frame(nil = 8.01 - tol,
tb = 0.01,
mito = 10)),
matches("Indeterminate - high nil")
)
expect_that(qft.criteria.070(data.frame(nil = 8.01 + tol,
tb = 0.01,
mito = 10)),
matches("Indeterminate - high nil")
)
# tb - nil ~ 0.70
expect_that(qft.criteria.070(data.frame(nil = 0.13,
tb = 0.83,
mito = 10)),
matches("Positive")
)
expect_that(qft.criteria.070(data.frame(nil = 0.13 - tol,
tb = 0.83,
mito = 10)),
matches("Positive")
)
expect_that(qft.criteria.070(data.frame(nil = 0.13 + tol,
tb = 0.83,
mito = 10)),
matches("Positive")
)
# tb - nil ~ 0.25*nil
expect_that(qft.criteria.070(data.frame(nil = 3.23,
tb = 3.23 + (3.23 * 0.25),
mito = 10)),
matches("Positive")
)
expect_that(qft.criteria.070(data.frame(nil = 3.23 - tol,
tb = 3.23 + (3.23 * 0.25),
mito = 10)),
matches("Positive")
)
expect_that(qft.criteria.070(data.frame(nil = 3.23 + tol,
tb = 3.23 + (3.23 * 0.25),
mito = 10)),
matches("Negative")
)
# mito - nil ~ 0.5
expect_that(qft.criteria.070(data.frame(nil = 0.50,
tb = 0.01,
mito = 1.00)),
matches("Negative")
)
expect_that(qft.criteria.070(data.frame(nil = 0.50 + tol,
tb = 0.01,
mito = 1.00)),
matches("Negative")
)
expect_that(qft.criteria.070(data.frame(nil = 0.50 - tol,
tb = 0.01,
mito = 1.00)),
matches("Negative")
)
})
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