Nothing
tests/testthat/test-class_summary.R
In rpact: Confirmatory Adaptive Clinical Trial Design and Analysis
## |
## | *Unit tests*
## |
## | This file is part of the R package rpact:
## | Confirmatory Adaptive Clinical Trial Design and Analysis
## |
## | Author: Gernot Wassmer, PhD, and Friedrich Pahlke, PhD
## | Licensed under "GNU Lesser General Public License" version 3
## | License text can be found here: https://www.r-project.org/Licenses/LGPL-3
## |
## | RPACT company website: https://www.rpact.com
## | RPACT package website: https://www.rpact.org
## |
## | Contact us for information about our services: info@rpact.com
## |
## | File name: test-class_summary.R
## | Creation date: 08 November 2023, 08:49:48
## | File version: $Revision$
## | Last changed: $Date$
## | Last changed by: $Author$
## |
test_plan_section("Testing Class 'SummaryFactory'")
test_that("Testing 'summary.ParameterSet': no errors occur", {
.skipTestIfDisabled()
# @refFS[Function]{fs:outputOfGenericFunctions}
invisible(capture.output(expect_error(summary(getDesignGroupSequential(
beta = 0.05, typeOfDesign = "asKD", gammaA = 1, typeBetaSpending = "bsOF"
)), NA)))
invisible(capture.output(expect_error(summary(getDesignGroupSequential(kMax = 1)), NA)))
invisible(capture.output(expect_error(summary(getDesignGroupSequential(kMax = 4, sided = 2)), NA)))
invisible(capture.output(expect_error(summary(getDesignGroupSequential(kMax = 4, sided = 2), digits = 0), NA)))
invisible(capture.output(expect_error(summary(getDesignGroupSequential(kMax = 1, sided = 2)), NA)))
invisible(capture.output(expect_error(summary(getDesignGroupSequential(futilityBounds = c(-6, 0))), NA)))
invisible(capture.output(expect_error(summary(getDesignGroupSequential(futilityBounds = c(-6, 0)), digits = 5), NA)))
invisible(capture.output(expect_error(summary(getDataset(
n = c(13, 25),
means = c(242, 222),
stDevs = c(244, 221)
)), NA)))
invisible(capture.output(expect_error(summary(getDataset(
n = c(13),
means = c(242),
stDevs = c(244)
)), NA)))
invisible(capture.output(expect_error(summary(getDataset(
n1 = c(13, 25),
n2 = c(15, NA),
n3 = c(14, 27),
n4 = c(12, 29),
means1 = c(242, 222),
means2 = c(188, NA),
means3 = c(267, 277),
means4 = c(92, 122),
stDevs1 = c(244, 221),
stDevs2 = c(212, NA),
stDevs3 = c(256, 232),
stDevs4 = c(215, 227)
)), NA)))
invisible(capture.output(expect_error(summary(getDataset(
n1 = c(11, 13, 12, 13),
n2 = c(8, 10, 9, 11),
n3 = c(7, 10, 8, 9),
events1 = c(10, 10, 12, 12),
events2 = c(3, 5, 5, 6),
events3 = c(2, 4, 3, 5)
)), NA)))
invisible(capture.output(expect_error(summary(getDataset(
events1 = c(25, 32),
events2 = c(18, NA),
events3 = c(22, 36),
logRanks1 = c(2.2, 1.8),
logRanks2 = c(1.99, NA),
logRanks3 = c(2.32, 2.11)
)), NA)))
invisible(capture.output(expect_error(summary(getDesignInverseNormal(kMax = 1)), NA)))
invisible(capture.output(expect_error(summary(getDesignInverseNormal(futilityBounds = c(0, 1))), NA)))
invisible(capture.output(expect_error(summary(getDesignInverseNormal(kMax = 1)), NA)))
invisible(capture.output(expect_error(summary(getDesignInverseNormal(kMax = 4, sided = 2)), NA)))
invisible(capture.output(expect_error(summary(getDesignInverseNormal(kMax = 4, sided = 2), digits = 0), NA)))
invisible(capture.output(expect_error(summary(getDesignInverseNormal(kMax = 1, sided = 2)), NA)))
invisible(capture.output(expect_error(summary(getDesignFisher()), NA)))
invisible(capture.output(expect_error(summary(getDesignFisher(alpha0Vec = c(0.1, 0.2))), NA)))
invisible(capture.output(expect_error(summary(getDesignFisher(kMax = 1)), NA)))
invisible(capture.output(expect_error(summary(getDesignFisher(kMax = 4), digits = 5), NA)))
invisible(capture.output(expect_error(summary(getDesignFisher(kMax = 4), digits = 0), NA)))
invisible(capture.output(expect_error(summary(getDesignFisher(kMax = 1)), NA)))
## test design plans - means
invisible(capture.output(expect_error(summary(getSampleSizeMeans(sided = 2, alternative = -0.5)), NA)))
invisible(capture.output(expect_warning(summary(getSampleSizeMeans(sided = 2), alternative = -0.5)))) # warning expected
invisible(capture.output(expect_error(summary(getPowerMeans(
sided = 1, alternative = c(-0.5, -0.3),
maxNumberOfSubjects = 100, directionUpper = FALSE
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
thetaH0 = 0,
alternative = 0.5, sided = 1, stDev = 2.5
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
thetaH0 = 0,
alternative = 0.5, sided = 1, stDev = 1, groups = 1
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
thetaH0 = 0,
sided = 2, stDev = 1, groups = 1
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
thetaH0 = 0,
alternative = 1.2, sided = 2, stDev = 5
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
thetaH0 = 0,
alternative = 1.2, sided = 2, stDev = 5, allocationRatioPlanned = 0
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
thetaH0 = 0,
alternative = 1.2, sided = 2, stDev = 5, groups = 1
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
), digits = 0), NA)))
invisible(capture.output(expect_error(summary(getPowerMeans(
getDesignGroupSequential(futilityBounds = c(1, 2)),
maxNumberOfSubjects = 100, alternative = 1
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
getDesignGroupSequential(kMax = 4, sided = 2)
)), NA)))
invisible(capture.output(expect_error(summary(getPowerMeans(
getDesignGroupSequential(kMax = 4, sided = 2),
maxNumberOfSubjects = 100
)), NA)))
invisible(capture.output(expect_error(summary(getPowerMeans(
getDesignGroupSequential(kMax = 1, sided = 2),
maxNumberOfSubjects = 100
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
), digits = 4), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
), digits = 3), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
), digits = 2), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
), digits = -1), NA)))
## test design plans - rates
invisible(capture.output(expect_error(summary(getSampleSizeRates(pi2 = 0.3)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(groups = 1, thetaH0 = 0.3)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(groups = 1, thetaH0 = 0.45)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(
groups = 2, thetaH0 = 0.45, allocationRatioPlanned = 0
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(
getDesignGroupSequential(futilityBounds = c(1, 2))
)), NA)))
invisible(capture.output(expect_error(summary(getPowerRates(
getDesignGroupSequential(futilityBounds = c(1, 2)),
maxNumberOfSubjects = 100
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(
getDesignGroupSequential(kMax = 4, sided = 2)
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(
getDesignGroupSequential(kMax = 4, sided = 2),
groups = 1, thetaH0 = 0.3
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(
getDesignGroupSequential(kMax = 1, sided = 2),
groups = 1, thetaH0 = 0.2, pi1 = c(0.4, 0.5)
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(
getDesignGroupSequential(kMax = 1, sided = 2),
groups = 1, thetaH0 = 0.2, pi1 = 0.4
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(
getDesignGroupSequential(kMax = 1, sided = 2),
groups = 2, thetaH0 = 0, pi1 = 0.25
)), NA)))
invisible(capture.output(expect_error(summary(getPowerRates(
getDesignGroupSequential(kMax = 4, sided = 2),
maxNumberOfSubjects = 100
)), NA)))
## test design plans - survival
invisible(capture.output(expect_error(summary(getSampleSizeSurvival()), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(lambda2 = 0.3, hazardRatio = 1.2)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(lambda2 = 0.3, hazardRatio = c(1.2, 2))), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(pi2 = 0.3, hazardRatio = 1.2)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(pi1 = 0.1, pi2 = 0.3)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(lambda2 = 0.03, lambda1 = c(0.040))), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(piecewiseSurvivalTime = list(
"0 - <6" = 0.025,
"6 - <9" = 0.04,
"9 - <15" = 0.015,
"15 - <21" = 0.01,
">=21" = 0.007
), hazardRatio = 1.2)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(
getDesignGroupSequential(futilityBounds = c(1, 2))
)), NA)))
invisible(capture.output(expect_error(summary(getPowerSurvival(
getDesignGroupSequential(futilityBounds = c(1, 2)),
maxNumberOfSubjects = 100, maxNumberOfEvents = 60
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(
getDesignGroupSequential(kMax = 4, sided = 2)
)), NA)))
invisible(capture.output(expect_error(summary(getPowerSurvival(
getDesignGroupSequential(kMax = 4, sided = 2),
maxNumberOfSubjects = 100, maxNumberOfEvents = 60
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(sided = 2, lambda2 = log(2) / 6, lambda1 = log(2) / 8)), NA)))
invisible(capture.output(expect_error(summary(getPowerSurvival(sided = 2, maxNumberOfSubjects = 200, maxNumberOfEvents = 40, lambda2 = log(2) / 6, lambda1 = log(2) / 8)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(
getDesignGroupSequential(sided = 2),
lambda2 = log(2) / 6, hazardRatio = c(0.55),
accrualTime = c(0, 10), accrualIntensity = 20
)), NA)))
invisible(capture.output(expect_error(summary(getPowerSurvival(
getDesignGroupSequential(kMax = 2),
maxNumberOfEvents = 200, maxNumberOfSubjects = 400,
lambda2 = log(2) / 60, lambda1 = log(2) / 50,
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30
)), NA)))
invisible(capture.output(expect_error(summary(getPowerSurvival(
getDesignGroupSequential(kMax = 3),
maxNumberOfEvents = 200, maxNumberOfSubjects = 400,
lambda2 = log(2) / 60, lambda1 = c(log(2) / 50, log(2) / 60),
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30
)), NA)))
invisible(capture.output(expect_error(summary(getPowerSurvival(
getDesignGroupSequential(kMax = 3),
maxNumberOfEvents = 200, maxNumberOfSubjects = 400,
lambda2 = log(2) / 60, hazardRatio = c(0.7, 0.8), directionUpper = FALSE,
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30
)), NA)))
design1 <- getDesignGroupSequential(
sided = 2, alpha = 0.05, beta = 0.2,
informationRates = c(0.6, 1),
typeOfDesign = "asOF", twoSidedPower = FALSE
)
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(
design1,
lambda2 = log(2) / 60, hazardRatio = 0.74,
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30,
followUpTime = 12
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(
design1,
lambda2 = log(2) / 60, lambda1 = log(2) / 50,
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30,
followUpTime = 12
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(
getDesignGroupSequential(kMax = 4, sided = 2)
)), NA)))
## simulations
design2 <- getDesignInverseNormal(
alpha = 0.05, kMax = 4, futilityBounds = c(0, 0, 0),
sided = 1, typeOfDesign = "WT", deltaWT = 0.1
)
invisible(capture.output(expect_error(summary(getSimulationSurvival(design2,
lambda2 = log(2) / 60, lambda1 = c(log(2) / 80),
maxNumberOfSubjects = 1000, plannedEvents = c(50, 100, 150, 200), seed = 12345, directionUpper = FALSE
)), NA)))
invisible(capture.output(expect_error(summary(getSimulationSurvival(design2,
lambda2 = log(2) / 60, hazardRatio = c(1.2, 1.4),
maxNumberOfSubjects = 1000, plannedEvents = c(50, 100, 150, 200), seed = 12345
)), NA)))
design3 <- getDesignGroupSequential(typeOfDesign = "P", futilityBounds = c(1, 1))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(design3)), NA)))
invisible(capture.output(expect_error(summary(getSimulationMeans(design3, stDev = 4, plannedSubjects = (1:3) * 200, alternative = c(1, 2))), NA)))
invisible(capture.output(expect_error(summary(getSimulationRates(design3,
plannedSubjects = (1:3) * 200, pi1 = c(0.3, 0.4), maxNumberOfIterations = 1000,
minNumberOfSubjectsPerStage = c(NA, 40, 40), maxNumberOfSubjectsPerStage = c(NA, 40, 400), conditionalPower = 0.8
)), NA)))
invisible(capture.output(expect_error(summary(getSimulationMeans(
getDesignGroupSequential(kMax = 1),
stDev = 4, plannedSubjects = 200, alternative = c(1)
)), NA)))
})
test_that("Testing 'summary.ParameterSet': output will be produced", {
.skipTestIfDisabled()
# @refFS[Function]{fs:outputOfGenericFunctions}
expect_output(summary(getDesignGroupSequential(beta = 0.05, typeOfDesign = "asKD", gammaA = 1, typeBetaSpending = "bsOF"))$show())
expect_output(summary(getDesignGroupSequential(kMax = 1))$show())
expect_output(summary(getDesignGroupSequential(kMax = 4, sided = 2))$show())
expect_output(summary(getDesignGroupSequential(kMax = 4, sided = 2), digits = 0)$show())
expect_output(summary(getDesignGroupSequential(kMax = 1, sided = 2))$show())
expect_output(summary(getDesignGroupSequential(futilityBounds = c(-6, 0)))$show())
expect_output(summary(getDesignGroupSequential(futilityBounds = c(-6, 0)), digits = 5)$show())
expect_output(summary(getDataset(
n = c(13, 25),
means = c(242, 222),
stDevs = c(244, 221)
))$show())
expect_output(summary(getDataset(
n = c(13),
means = c(242),
stDevs = c(244)
))$show())
expect_output(summary(getDataset(
n1 = c(13, 25),
n2 = c(15, NA),
n3 = c(14, 27),
n4 = c(12, 29),
means1 = c(242, 222),
means2 = c(188, NA),
means3 = c(267, 277),
means4 = c(92, 122),
stDevs1 = c(244, 221),
stDevs2 = c(212, NA),
stDevs3 = c(256, 232),
stDevs4 = c(215, 227)
))$show())
expect_output(summary(getDataset(
n1 = c(11, 13, 12, 13),
n2 = c(8, 10, 9, 11),
n3 = c(7, 10, 8, 9),
events1 = c(10, 10, 12, 12),
events2 = c(3, 5, 5, 6),
events3 = c(2, 4, 3, 5)
))$show())
expect_output(summary(getDataset(
events1 = c(25, 32),
events2 = c(18, NA),
events3 = c(22, 36),
logRanks1 = c(2.2, 1.8),
logRanks2 = c(1.99, NA),
logRanks3 = c(2.32, 2.11)
))$show())
expect_output(summary(getDesignInverseNormal(kMax = 1))$show())
expect_output(summary(getDesignInverseNormal(futilityBounds = c(0, 1)))$show())
expect_output(summary(getDesignInverseNormal(kMax = 1))$show())
expect_output(summary(getDesignInverseNormal(kMax = 4, sided = 2))$show())
expect_output(summary(getDesignInverseNormal(kMax = 4, sided = 2), digits = 0)$show())
expect_output(summary(getDesignInverseNormal(kMax = 1, sided = 2))$show())
expect_output(summary(getDesignFisher())$show())
expect_output(summary(getDesignFisher(alpha0Vec = c(0.1, 0.2)))$show())
expect_output(summary(getDesignFisher(kMax = 1))$show())
expect_output(summary(getDesignFisher(kMax = 4), digits = 5)$show())
expect_output(summary(getDesignFisher(kMax = 4), digits = 0)$show())
expect_output(summary(getDesignFisher(kMax = 1))$show())
## test design plans - means
expect_output(summary(getSampleSizeMeans(sided = 2, alternative = -0.5))$show())
expect_output(summary(getPowerMeans(sided = 1, alternative = c(-0.5, -0.3), maxNumberOfSubjects = 100, directionUpper = FALSE))$show())
expect_output(summary(getSampleSizeMeans(thetaH0 = 0, alternative = 0.5, sided = 1, stDev = 2.5))$show())
expect_output(summary(getSampleSizeMeans(thetaH0 = 0, alternative = 0.5, sided = 1, stDev = 1, groups = 1))$show())
expect_output(summary(getSampleSizeMeans(thetaH0 = 0, sided = 2, stDev = 1, groups = 1))$show())
expect_output(summary(getSampleSizeMeans(thetaH0 = 0, alternative = 1.2, sided = 2, stDev = 5))$show())
expect_output(summary(getSampleSizeMeans(thetaH0 = 0, alternative = 1.2, sided = 2, stDev = 5, allocationRatioPlanned = 0))$show())
expect_output(summary(getSampleSizeMeans(thetaH0 = 0, alternative = 1.2, sided = 2, stDev = 5, groups = 1))$show())
expect_output(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
))$show())
expect_output(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
), digits = 0)$show())
expect_output(summary(getPowerMeans(
getDesignGroupSequential(futilityBounds = c(1, 2)),
maxNumberOfSubjects = 100, alternative = 1
))$show())
expect_output(summary(getSampleSizeMeans(
getDesignGroupSequential(kMax = 4, sided = 2)
))$show())
expect_output(summary(getPowerMeans(
getDesignGroupSequential(kMax = 4, sided = 2),
maxNumberOfSubjects = 100
))$show())
expect_output(summary(getPowerMeans(
getDesignGroupSequential(kMax = 1, sided = 2),
maxNumberOfSubjects = 100
))$show())
expect_output(summary(getSampleSizeMeans(getDesignGroupSequential(futilityBounds = c(1, 2))))$show())
expect_output(summary(getSampleSizeMeans(getDesignGroupSequential(futilityBounds = c(1, 2))), digits = 4)$show())
expect_output(summary(getSampleSizeMeans(getDesignGroupSequential(futilityBounds = c(1, 2))), digits = 3)$show())
expect_output(summary(getSampleSizeMeans(getDesignGroupSequential(futilityBounds = c(1, 2))), digits = 2)$show())
expect_output(summary(getSampleSizeMeans(getDesignGroupSequential(futilityBounds = c(1, 2))), digits = -1)$show())
## test design plans - rates
expect_output(summary(getSampleSizeRates(pi2 = 0.3))$show())
expect_output(summary(getSampleSizeRates(groups = 1, thetaH0 = 0.3))$show())
expect_output(summary(getSampleSizeRates(groups = 1, thetaH0 = 0.45))$show())
expect_output(summary(getSampleSizeRates(groups = 2, thetaH0 = 0.45, allocationRatioPlanned = 0))$show())
expect_output(summary(getSampleSizeRates(getDesignGroupSequential(futilityBounds = c(1, 2))))$show())
expect_output(summary(getPowerRates(getDesignGroupSequential(futilityBounds = c(1, 2)), maxNumberOfSubjects = 100))$show())
expect_output(summary(getSampleSizeRates(getDesignGroupSequential(kMax = 4, sided = 2)))$show())
expect_output(summary(getSampleSizeRates(getDesignGroupSequential(kMax = 4, sided = 2), groups = 1, thetaH0 = 0.3))$show())
expect_output(summary(getSampleSizeRates(getDesignGroupSequential(kMax = 1, sided = 2),
groups = 1, thetaH0 = 0.2, pi1 = c(0.4, 0.5)
))$show())
expect_output(summary(getSampleSizeRates(getDesignGroupSequential(
kMax = 1, sided = 2
), groups = 1, thetaH0 = 0.2, pi1 = 0.4))$show())
expect_output(summary(getSampleSizeRates(getDesignGroupSequential(
kMax = 1, sided = 2
), groups = 2, thetaH0 = 0, pi1 = 0.25))$show())
expect_output(summary(getPowerRates(getDesignGroupSequential(kMax = 4, sided = 2), maxNumberOfSubjects = 100))$show())
## test design plans - survival
expect_output(summary(getSampleSizeSurvival())$show())
expect_output(summary(getSampleSizeSurvival(lambda2 = 0.3, hazardRatio = 1.2))$show())
expect_output(summary(getSampleSizeSurvival(lambda2 = 0.3, hazardRatio = c(1.2, 2)))$show())
expect_output(summary(getSampleSizeSurvival(pi2 = 0.3, hazardRatio = 1.2))$show())
expect_output(summary(getSampleSizeSurvival(pi1 = 0.1, pi2 = 0.3))$show())
expect_output(summary(getSampleSizeSurvival(lambda2 = 0.03, lambda1 = c(0.040)))$show())
expect_output(summary(getSampleSizeSurvival(piecewiseSurvivalTime = list(
"0 - <6" = 0.025,
"6 - <9" = 0.04,
"9 - <15" = 0.015,
"15 - <21" = 0.01,
">=21" = 0.007
), hazardRatio = 1.2))$show())
expect_output(summary(getSampleSizeSurvival(getDesignGroupSequential(futilityBounds = c(1, 2))))$show())
expect_output(summary(getPowerSurvival(getDesignGroupSequential(futilityBounds = c(1, 2)),
maxNumberOfSubjects = 100, maxNumberOfEvents = 60
))$show())
expect_output(summary(getSampleSizeSurvival(getDesignGroupSequential(kMax = 4, sided = 2)))$show())
expect_output(summary(getPowerSurvival(getDesignGroupSequential(kMax = 4, sided = 2),
maxNumberOfSubjects = 100, maxNumberOfEvents = 60
))$show())
expect_output(summary(getSampleSizeSurvival(sided = 2, lambda2 = log(2) / 6, lambda1 = log(2) / 8))$show())
expect_output(summary(getPowerSurvival(
sided = 2, maxNumberOfSubjects = 200,
maxNumberOfEvents = 40, lambda2 = log(2) / 6, lambda1 = log(2) / 8
))$show())
expect_warning(expect_output(summary(getSampleSizeSurvival(getDesignGroupSequential(sided = 2),
lambda2 = log(2) / 6, hazardRatio = c(0.55),
accrualTime = c(0, 10), accrualIntensity = 60
))$show()),
"Accrual duration longer than maximal study duration (time to maximal number of events); followUpTime = -2.959",
fixed = TRUE
)
expect_output(summary(getPowerSurvival(getDesignGroupSequential(kMax = 2),
maxNumberOfEvents = 150, maxNumberOfSubjects = 400,
lambda2 = log(2) / 60, lambda1 = log(2) / 50,
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30
))$show())
expect_output(summary(getPowerSurvival(getDesignGroupSequential(kMax = 3),
maxNumberOfEvents = 200, maxNumberOfSubjects = 400,
lambda2 = log(2) / 60, lambda1 = c(log(2) / 50, log(2) / 60),
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30
))$show())
expect_output(summary(getPowerSurvival(getDesignGroupSequential(kMax = 3),
maxNumberOfEvents = 200, maxNumberOfSubjects = 400,
lambda2 = log(2) / 60, hazardRatio = c(0.7, 0.8), directionUpper = FALSE,
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30
))$show())
design1 <- getDesignGroupSequential(
sided = 2, alpha = 0.05, beta = 0.2,
informationRates = c(0.6, 1),
typeOfDesign = "asOF", twoSidedPower = FALSE
)
expect_output(summary(getSampleSizeSurvival(
design1,
lambda2 = log(2) / 60, hazardRatio = 0.74,
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30,
followUpTime = 12
))$show())
expect_output(summary(getSampleSizeSurvival(
design1,
lambda2 = log(2) / 60, lambda1 = log(2) / 50,
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30,
followUpTime = 12
))$show())
expect_output(summary(getSampleSizeSurvival(getDesignGroupSequential(kMax = 4, sided = 2)))$show())
## simulations
design2 <- getDesignInverseNormal(
alpha = 0.05, kMax = 4, futilityBounds = c(0, 0, 0),
sided = 1, typeOfDesign = "WT", deltaWT = 0.1
)
expect_output(summary(getSimulationSurvival(design2,
lambda2 = log(2) / 60, lambda1 = c(log(2) / 80),
maxNumberOfSubjects = 1000, plannedEvents = c(50, 100, 150, 200), seed = 12345, directionUpper = FALSE
))$show())
expect_output(summary(getSimulationSurvival(design2,
lambda2 = log(2) / 60, hazardRatio = c(1.2, 1.4),
maxNumberOfSubjects = 1000, plannedEvents = c(50, 100, 150, 200), seed = 12345
))$show())
design3 <- getDesignGroupSequential(typeOfDesign = "P", futilityBounds = c(1, 1))
expect_output(summary(getSampleSizeMeans(design3))$show())
expect_output(summary(getSimulationMeans(design3, stDev = 4, plannedSubjects = (1:3) * 200, alternative = c(1, 2)))$show())
expect_output(summary(getSimulationRates(design3,
plannedSubjects = (1:3) * 200, pi1 = c(0.3, 0.4), maxNumberOfIterations = 1000,
minNumberOfSubjectsPerStage = c(NA, 40, 40), maxNumberOfSubjectsPerStage = c(NA, 40, 400), conditionalPower = 0.8
))$show())
expect_output(summary(getSimulationMeans(getDesignGroupSequential(kMax = 1),
stDev = 4, plannedSubjects = 200, alternative = 1
))$show())
})
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## |
## | *Unit tests*
## |
## | This file is part of the R package rpact:
## | Confirmatory Adaptive Clinical Trial Design and Analysis
## |
## | Author: Gernot Wassmer, PhD, and Friedrich Pahlke, PhD
## | Licensed under "GNU Lesser General Public License" version 3
## | License text can be found here: https://www.r-project.org/Licenses/LGPL-3
## |
## | RPACT company website: https://www.rpact.com
## | RPACT package website: https://www.rpact.org
## |
## | Contact us for information about our services: info@rpact.com
## |
## | File name: test-class_summary.R
## | Creation date: 08 November 2023, 08:49:48
## | File version: $Revision$
## | Last changed: $Date$
## | Last changed by: $Author$
## |
test_plan_section("Testing Class 'SummaryFactory'")
test_that("Testing 'summary.ParameterSet': no errors occur", {
.skipTestIfDisabled()
# @refFS[Function]{fs:outputOfGenericFunctions}
invisible(capture.output(expect_error(summary(getDesignGroupSequential(
beta = 0.05, typeOfDesign = "asKD", gammaA = 1, typeBetaSpending = "bsOF"
)), NA)))
invisible(capture.output(expect_error(summary(getDesignGroupSequential(kMax = 1)), NA)))
invisible(capture.output(expect_error(summary(getDesignGroupSequential(kMax = 4, sided = 2)), NA)))
invisible(capture.output(expect_error(summary(getDesignGroupSequential(kMax = 4, sided = 2), digits = 0), NA)))
invisible(capture.output(expect_error(summary(getDesignGroupSequential(kMax = 1, sided = 2)), NA)))
invisible(capture.output(expect_error(summary(getDesignGroupSequential(futilityBounds = c(-6, 0))), NA)))
invisible(capture.output(expect_error(summary(getDesignGroupSequential(futilityBounds = c(-6, 0)), digits = 5), NA)))
invisible(capture.output(expect_error(summary(getDataset(
n = c(13, 25),
means = c(242, 222),
stDevs = c(244, 221)
)), NA)))
invisible(capture.output(expect_error(summary(getDataset(
n = c(13),
means = c(242),
stDevs = c(244)
)), NA)))
invisible(capture.output(expect_error(summary(getDataset(
n1 = c(13, 25),
n2 = c(15, NA),
n3 = c(14, 27),
n4 = c(12, 29),
means1 = c(242, 222),
means2 = c(188, NA),
means3 = c(267, 277),
means4 = c(92, 122),
stDevs1 = c(244, 221),
stDevs2 = c(212, NA),
stDevs3 = c(256, 232),
stDevs4 = c(215, 227)
)), NA)))
invisible(capture.output(expect_error(summary(getDataset(
n1 = c(11, 13, 12, 13),
n2 = c(8, 10, 9, 11),
n3 = c(7, 10, 8, 9),
events1 = c(10, 10, 12, 12),
events2 = c(3, 5, 5, 6),
events3 = c(2, 4, 3, 5)
)), NA)))
invisible(capture.output(expect_error(summary(getDataset(
events1 = c(25, 32),
events2 = c(18, NA),
events3 = c(22, 36),
logRanks1 = c(2.2, 1.8),
logRanks2 = c(1.99, NA),
logRanks3 = c(2.32, 2.11)
)), NA)))
invisible(capture.output(expect_error(summary(getDesignInverseNormal(kMax = 1)), NA)))
invisible(capture.output(expect_error(summary(getDesignInverseNormal(futilityBounds = c(0, 1))), NA)))
invisible(capture.output(expect_error(summary(getDesignInverseNormal(kMax = 1)), NA)))
invisible(capture.output(expect_error(summary(getDesignInverseNormal(kMax = 4, sided = 2)), NA)))
invisible(capture.output(expect_error(summary(getDesignInverseNormal(kMax = 4, sided = 2), digits = 0), NA)))
invisible(capture.output(expect_error(summary(getDesignInverseNormal(kMax = 1, sided = 2)), NA)))
invisible(capture.output(expect_error(summary(getDesignFisher()), NA)))
invisible(capture.output(expect_error(summary(getDesignFisher(alpha0Vec = c(0.1, 0.2))), NA)))
invisible(capture.output(expect_error(summary(getDesignFisher(kMax = 1)), NA)))
invisible(capture.output(expect_error(summary(getDesignFisher(kMax = 4), digits = 5), NA)))
invisible(capture.output(expect_error(summary(getDesignFisher(kMax = 4), digits = 0), NA)))
invisible(capture.output(expect_error(summary(getDesignFisher(kMax = 1)), NA)))
## test design plans - means
invisible(capture.output(expect_error(summary(getSampleSizeMeans(sided = 2, alternative = -0.5)), NA)))
invisible(capture.output(expect_warning(summary(getSampleSizeMeans(sided = 2), alternative = -0.5)))) # warning expected
invisible(capture.output(expect_error(summary(getPowerMeans(
sided = 1, alternative = c(-0.5, -0.3),
maxNumberOfSubjects = 100, directionUpper = FALSE
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
thetaH0 = 0,
alternative = 0.5, sided = 1, stDev = 2.5
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
thetaH0 = 0,
alternative = 0.5, sided = 1, stDev = 1, groups = 1
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
thetaH0 = 0,
sided = 2, stDev = 1, groups = 1
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
thetaH0 = 0,
alternative = 1.2, sided = 2, stDev = 5
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
thetaH0 = 0,
alternative = 1.2, sided = 2, stDev = 5, allocationRatioPlanned = 0
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
thetaH0 = 0,
alternative = 1.2, sided = 2, stDev = 5, groups = 1
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
), digits = 0), NA)))
invisible(capture.output(expect_error(summary(getPowerMeans(
getDesignGroupSequential(futilityBounds = c(1, 2)),
maxNumberOfSubjects = 100, alternative = 1
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
getDesignGroupSequential(kMax = 4, sided = 2)
)), NA)))
invisible(capture.output(expect_error(summary(getPowerMeans(
getDesignGroupSequential(kMax = 4, sided = 2),
maxNumberOfSubjects = 100
)), NA)))
invisible(capture.output(expect_error(summary(getPowerMeans(
getDesignGroupSequential(kMax = 1, sided = 2),
maxNumberOfSubjects = 100
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
), digits = 4), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
), digits = 3), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
), digits = 2), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
), digits = -1), NA)))
## test design plans - rates
invisible(capture.output(expect_error(summary(getSampleSizeRates(pi2 = 0.3)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(groups = 1, thetaH0 = 0.3)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(groups = 1, thetaH0 = 0.45)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(
groups = 2, thetaH0 = 0.45, allocationRatioPlanned = 0
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(
getDesignGroupSequential(futilityBounds = c(1, 2))
)), NA)))
invisible(capture.output(expect_error(summary(getPowerRates(
getDesignGroupSequential(futilityBounds = c(1, 2)),
maxNumberOfSubjects = 100
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(
getDesignGroupSequential(kMax = 4, sided = 2)
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(
getDesignGroupSequential(kMax = 4, sided = 2),
groups = 1, thetaH0 = 0.3
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(
getDesignGroupSequential(kMax = 1, sided = 2),
groups = 1, thetaH0 = 0.2, pi1 = c(0.4, 0.5)
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(
getDesignGroupSequential(kMax = 1, sided = 2),
groups = 1, thetaH0 = 0.2, pi1 = 0.4
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeRates(
getDesignGroupSequential(kMax = 1, sided = 2),
groups = 2, thetaH0 = 0, pi1 = 0.25
)), NA)))
invisible(capture.output(expect_error(summary(getPowerRates(
getDesignGroupSequential(kMax = 4, sided = 2),
maxNumberOfSubjects = 100
)), NA)))
## test design plans - survival
invisible(capture.output(expect_error(summary(getSampleSizeSurvival()), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(lambda2 = 0.3, hazardRatio = 1.2)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(lambda2 = 0.3, hazardRatio = c(1.2, 2))), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(pi2 = 0.3, hazardRatio = 1.2)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(pi1 = 0.1, pi2 = 0.3)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(lambda2 = 0.03, lambda1 = c(0.040))), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(piecewiseSurvivalTime = list(
"0 - <6" = 0.025,
"6 - <9" = 0.04,
"9 - <15" = 0.015,
"15 - <21" = 0.01,
">=21" = 0.007
), hazardRatio = 1.2)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(
getDesignGroupSequential(futilityBounds = c(1, 2))
)), NA)))
invisible(capture.output(expect_error(summary(getPowerSurvival(
getDesignGroupSequential(futilityBounds = c(1, 2)),
maxNumberOfSubjects = 100, maxNumberOfEvents = 60
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(
getDesignGroupSequential(kMax = 4, sided = 2)
)), NA)))
invisible(capture.output(expect_error(summary(getPowerSurvival(
getDesignGroupSequential(kMax = 4, sided = 2),
maxNumberOfSubjects = 100, maxNumberOfEvents = 60
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(sided = 2, lambda2 = log(2) / 6, lambda1 = log(2) / 8)), NA)))
invisible(capture.output(expect_error(summary(getPowerSurvival(sided = 2, maxNumberOfSubjects = 200, maxNumberOfEvents = 40, lambda2 = log(2) / 6, lambda1 = log(2) / 8)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(
getDesignGroupSequential(sided = 2),
lambda2 = log(2) / 6, hazardRatio = c(0.55),
accrualTime = c(0, 10), accrualIntensity = 20
)), NA)))
invisible(capture.output(expect_error(summary(getPowerSurvival(
getDesignGroupSequential(kMax = 2),
maxNumberOfEvents = 200, maxNumberOfSubjects = 400,
lambda2 = log(2) / 60, lambda1 = log(2) / 50,
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30
)), NA)))
invisible(capture.output(expect_error(summary(getPowerSurvival(
getDesignGroupSequential(kMax = 3),
maxNumberOfEvents = 200, maxNumberOfSubjects = 400,
lambda2 = log(2) / 60, lambda1 = c(log(2) / 50, log(2) / 60),
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30
)), NA)))
invisible(capture.output(expect_error(summary(getPowerSurvival(
getDesignGroupSequential(kMax = 3),
maxNumberOfEvents = 200, maxNumberOfSubjects = 400,
lambda2 = log(2) / 60, hazardRatio = c(0.7, 0.8), directionUpper = FALSE,
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30
)), NA)))
design1 <- getDesignGroupSequential(
sided = 2, alpha = 0.05, beta = 0.2,
informationRates = c(0.6, 1),
typeOfDesign = "asOF", twoSidedPower = FALSE
)
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(
design1,
lambda2 = log(2) / 60, hazardRatio = 0.74,
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30,
followUpTime = 12
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(
design1,
lambda2 = log(2) / 60, lambda1 = log(2) / 50,
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30,
followUpTime = 12
)), NA)))
invisible(capture.output(expect_error(summary(getSampleSizeSurvival(
getDesignGroupSequential(kMax = 4, sided = 2)
)), NA)))
## simulations
design2 <- getDesignInverseNormal(
alpha = 0.05, kMax = 4, futilityBounds = c(0, 0, 0),
sided = 1, typeOfDesign = "WT", deltaWT = 0.1
)
invisible(capture.output(expect_error(summary(getSimulationSurvival(design2,
lambda2 = log(2) / 60, lambda1 = c(log(2) / 80),
maxNumberOfSubjects = 1000, plannedEvents = c(50, 100, 150, 200), seed = 12345, directionUpper = FALSE
)), NA)))
invisible(capture.output(expect_error(summary(getSimulationSurvival(design2,
lambda2 = log(2) / 60, hazardRatio = c(1.2, 1.4),
maxNumberOfSubjects = 1000, plannedEvents = c(50, 100, 150, 200), seed = 12345
)), NA)))
design3 <- getDesignGroupSequential(typeOfDesign = "P", futilityBounds = c(1, 1))
invisible(capture.output(expect_error(summary(getSampleSizeMeans(design3)), NA)))
invisible(capture.output(expect_error(summary(getSimulationMeans(design3, stDev = 4, plannedSubjects = (1:3) * 200, alternative = c(1, 2))), NA)))
invisible(capture.output(expect_error(summary(getSimulationRates(design3,
plannedSubjects = (1:3) * 200, pi1 = c(0.3, 0.4), maxNumberOfIterations = 1000,
minNumberOfSubjectsPerStage = c(NA, 40, 40), maxNumberOfSubjectsPerStage = c(NA, 40, 400), conditionalPower = 0.8
)), NA)))
invisible(capture.output(expect_error(summary(getSimulationMeans(
getDesignGroupSequential(kMax = 1),
stDev = 4, plannedSubjects = 200, alternative = c(1)
)), NA)))
})
test_that("Testing 'summary.ParameterSet': output will be produced", {
.skipTestIfDisabled()
# @refFS[Function]{fs:outputOfGenericFunctions}
expect_output(summary(getDesignGroupSequential(beta = 0.05, typeOfDesign = "asKD", gammaA = 1, typeBetaSpending = "bsOF"))$show())
expect_output(summary(getDesignGroupSequential(kMax = 1))$show())
expect_output(summary(getDesignGroupSequential(kMax = 4, sided = 2))$show())
expect_output(summary(getDesignGroupSequential(kMax = 4, sided = 2), digits = 0)$show())
expect_output(summary(getDesignGroupSequential(kMax = 1, sided = 2))$show())
expect_output(summary(getDesignGroupSequential(futilityBounds = c(-6, 0)))$show())
expect_output(summary(getDesignGroupSequential(futilityBounds = c(-6, 0)), digits = 5)$show())
expect_output(summary(getDataset(
n = c(13, 25),
means = c(242, 222),
stDevs = c(244, 221)
))$show())
expect_output(summary(getDataset(
n = c(13),
means = c(242),
stDevs = c(244)
))$show())
expect_output(summary(getDataset(
n1 = c(13, 25),
n2 = c(15, NA),
n3 = c(14, 27),
n4 = c(12, 29),
means1 = c(242, 222),
means2 = c(188, NA),
means3 = c(267, 277),
means4 = c(92, 122),
stDevs1 = c(244, 221),
stDevs2 = c(212, NA),
stDevs3 = c(256, 232),
stDevs4 = c(215, 227)
))$show())
expect_output(summary(getDataset(
n1 = c(11, 13, 12, 13),
n2 = c(8, 10, 9, 11),
n3 = c(7, 10, 8, 9),
events1 = c(10, 10, 12, 12),
events2 = c(3, 5, 5, 6),
events3 = c(2, 4, 3, 5)
))$show())
expect_output(summary(getDataset(
events1 = c(25, 32),
events2 = c(18, NA),
events3 = c(22, 36),
logRanks1 = c(2.2, 1.8),
logRanks2 = c(1.99, NA),
logRanks3 = c(2.32, 2.11)
))$show())
expect_output(summary(getDesignInverseNormal(kMax = 1))$show())
expect_output(summary(getDesignInverseNormal(futilityBounds = c(0, 1)))$show())
expect_output(summary(getDesignInverseNormal(kMax = 1))$show())
expect_output(summary(getDesignInverseNormal(kMax = 4, sided = 2))$show())
expect_output(summary(getDesignInverseNormal(kMax = 4, sided = 2), digits = 0)$show())
expect_output(summary(getDesignInverseNormal(kMax = 1, sided = 2))$show())
expect_output(summary(getDesignFisher())$show())
expect_output(summary(getDesignFisher(alpha0Vec = c(0.1, 0.2)))$show())
expect_output(summary(getDesignFisher(kMax = 1))$show())
expect_output(summary(getDesignFisher(kMax = 4), digits = 5)$show())
expect_output(summary(getDesignFisher(kMax = 4), digits = 0)$show())
expect_output(summary(getDesignFisher(kMax = 1))$show())
## test design plans - means
expect_output(summary(getSampleSizeMeans(sided = 2, alternative = -0.5))$show())
expect_output(summary(getPowerMeans(sided = 1, alternative = c(-0.5, -0.3), maxNumberOfSubjects = 100, directionUpper = FALSE))$show())
expect_output(summary(getSampleSizeMeans(thetaH0 = 0, alternative = 0.5, sided = 1, stDev = 2.5))$show())
expect_output(summary(getSampleSizeMeans(thetaH0 = 0, alternative = 0.5, sided = 1, stDev = 1, groups = 1))$show())
expect_output(summary(getSampleSizeMeans(thetaH0 = 0, sided = 2, stDev = 1, groups = 1))$show())
expect_output(summary(getSampleSizeMeans(thetaH0 = 0, alternative = 1.2, sided = 2, stDev = 5))$show())
expect_output(summary(getSampleSizeMeans(thetaH0 = 0, alternative = 1.2, sided = 2, stDev = 5, allocationRatioPlanned = 0))$show())
expect_output(summary(getSampleSizeMeans(thetaH0 = 0, alternative = 1.2, sided = 2, stDev = 5, groups = 1))$show())
expect_output(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
))$show())
expect_output(summary(getSampleSizeMeans(
getDesignGroupSequential(futilityBounds = c(1, 2))
), digits = 0)$show())
expect_output(summary(getPowerMeans(
getDesignGroupSequential(futilityBounds = c(1, 2)),
maxNumberOfSubjects = 100, alternative = 1
))$show())
expect_output(summary(getSampleSizeMeans(
getDesignGroupSequential(kMax = 4, sided = 2)
))$show())
expect_output(summary(getPowerMeans(
getDesignGroupSequential(kMax = 4, sided = 2),
maxNumberOfSubjects = 100
))$show())
expect_output(summary(getPowerMeans(
getDesignGroupSequential(kMax = 1, sided = 2),
maxNumberOfSubjects = 100
))$show())
expect_output(summary(getSampleSizeMeans(getDesignGroupSequential(futilityBounds = c(1, 2))))$show())
expect_output(summary(getSampleSizeMeans(getDesignGroupSequential(futilityBounds = c(1, 2))), digits = 4)$show())
expect_output(summary(getSampleSizeMeans(getDesignGroupSequential(futilityBounds = c(1, 2))), digits = 3)$show())
expect_output(summary(getSampleSizeMeans(getDesignGroupSequential(futilityBounds = c(1, 2))), digits = 2)$show())
expect_output(summary(getSampleSizeMeans(getDesignGroupSequential(futilityBounds = c(1, 2))), digits = -1)$show())
## test design plans - rates
expect_output(summary(getSampleSizeRates(pi2 = 0.3))$show())
expect_output(summary(getSampleSizeRates(groups = 1, thetaH0 = 0.3))$show())
expect_output(summary(getSampleSizeRates(groups = 1, thetaH0 = 0.45))$show())
expect_output(summary(getSampleSizeRates(groups = 2, thetaH0 = 0.45, allocationRatioPlanned = 0))$show())
expect_output(summary(getSampleSizeRates(getDesignGroupSequential(futilityBounds = c(1, 2))))$show())
expect_output(summary(getPowerRates(getDesignGroupSequential(futilityBounds = c(1, 2)), maxNumberOfSubjects = 100))$show())
expect_output(summary(getSampleSizeRates(getDesignGroupSequential(kMax = 4, sided = 2)))$show())
expect_output(summary(getSampleSizeRates(getDesignGroupSequential(kMax = 4, sided = 2), groups = 1, thetaH0 = 0.3))$show())
expect_output(summary(getSampleSizeRates(getDesignGroupSequential(kMax = 1, sided = 2),
groups = 1, thetaH0 = 0.2, pi1 = c(0.4, 0.5)
))$show())
expect_output(summary(getSampleSizeRates(getDesignGroupSequential(
kMax = 1, sided = 2
), groups = 1, thetaH0 = 0.2, pi1 = 0.4))$show())
expect_output(summary(getSampleSizeRates(getDesignGroupSequential(
kMax = 1, sided = 2
), groups = 2, thetaH0 = 0, pi1 = 0.25))$show())
expect_output(summary(getPowerRates(getDesignGroupSequential(kMax = 4, sided = 2), maxNumberOfSubjects = 100))$show())
## test design plans - survival
expect_output(summary(getSampleSizeSurvival())$show())
expect_output(summary(getSampleSizeSurvival(lambda2 = 0.3, hazardRatio = 1.2))$show())
expect_output(summary(getSampleSizeSurvival(lambda2 = 0.3, hazardRatio = c(1.2, 2)))$show())
expect_output(summary(getSampleSizeSurvival(pi2 = 0.3, hazardRatio = 1.2))$show())
expect_output(summary(getSampleSizeSurvival(pi1 = 0.1, pi2 = 0.3))$show())
expect_output(summary(getSampleSizeSurvival(lambda2 = 0.03, lambda1 = c(0.040)))$show())
expect_output(summary(getSampleSizeSurvival(piecewiseSurvivalTime = list(
"0 - <6" = 0.025,
"6 - <9" = 0.04,
"9 - <15" = 0.015,
"15 - <21" = 0.01,
">=21" = 0.007
), hazardRatio = 1.2))$show())
expect_output(summary(getSampleSizeSurvival(getDesignGroupSequential(futilityBounds = c(1, 2))))$show())
expect_output(summary(getPowerSurvival(getDesignGroupSequential(futilityBounds = c(1, 2)),
maxNumberOfSubjects = 100, maxNumberOfEvents = 60
))$show())
expect_output(summary(getSampleSizeSurvival(getDesignGroupSequential(kMax = 4, sided = 2)))$show())
expect_output(summary(getPowerSurvival(getDesignGroupSequential(kMax = 4, sided = 2),
maxNumberOfSubjects = 100, maxNumberOfEvents = 60
))$show())
expect_output(summary(getSampleSizeSurvival(sided = 2, lambda2 = log(2) / 6, lambda1 = log(2) / 8))$show())
expect_output(summary(getPowerSurvival(
sided = 2, maxNumberOfSubjects = 200,
maxNumberOfEvents = 40, lambda2 = log(2) / 6, lambda1 = log(2) / 8
))$show())
expect_warning(expect_output(summary(getSampleSizeSurvival(getDesignGroupSequential(sided = 2),
lambda2 = log(2) / 6, hazardRatio = c(0.55),
accrualTime = c(0, 10), accrualIntensity = 60
))$show()),
"Accrual duration longer than maximal study duration (time to maximal number of events); followUpTime = -2.959",
fixed = TRUE
)
expect_output(summary(getPowerSurvival(getDesignGroupSequential(kMax = 2),
maxNumberOfEvents = 150, maxNumberOfSubjects = 400,
lambda2 = log(2) / 60, lambda1 = log(2) / 50,
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30
))$show())
expect_output(summary(getPowerSurvival(getDesignGroupSequential(kMax = 3),
maxNumberOfEvents = 200, maxNumberOfSubjects = 400,
lambda2 = log(2) / 60, lambda1 = c(log(2) / 50, log(2) / 60),
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30
))$show())
expect_output(summary(getPowerSurvival(getDesignGroupSequential(kMax = 3),
maxNumberOfEvents = 200, maxNumberOfSubjects = 400,
lambda2 = log(2) / 60, hazardRatio = c(0.7, 0.8), directionUpper = FALSE,
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30
))$show())
design1 <- getDesignGroupSequential(
sided = 2, alpha = 0.05, beta = 0.2,
informationRates = c(0.6, 1),
typeOfDesign = "asOF", twoSidedPower = FALSE
)
expect_output(summary(getSampleSizeSurvival(
design1,
lambda2 = log(2) / 60, hazardRatio = 0.74,
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30,
followUpTime = 12
))$show())
expect_output(summary(getSampleSizeSurvival(
design1,
lambda2 = log(2) / 60, lambda1 = log(2) / 50,
dropoutRate1 = 0.025, dropoutRate2 = 0.025, dropoutTime = 12,
accrualTime = 0, accrualIntensity = 30,
followUpTime = 12
))$show())
expect_output(summary(getSampleSizeSurvival(getDesignGroupSequential(kMax = 4, sided = 2)))$show())
## simulations
design2 <- getDesignInverseNormal(
alpha = 0.05, kMax = 4, futilityBounds = c(0, 0, 0),
sided = 1, typeOfDesign = "WT", deltaWT = 0.1
)
expect_output(summary(getSimulationSurvival(design2,
lambda2 = log(2) / 60, lambda1 = c(log(2) / 80),
maxNumberOfSubjects = 1000, plannedEvents = c(50, 100, 150, 200), seed = 12345, directionUpper = FALSE
))$show())
expect_output(summary(getSimulationSurvival(design2,
lambda2 = log(2) / 60, hazardRatio = c(1.2, 1.4),
maxNumberOfSubjects = 1000, plannedEvents = c(50, 100, 150, 200), seed = 12345
))$show())
design3 <- getDesignGroupSequential(typeOfDesign = "P", futilityBounds = c(1, 1))
expect_output(summary(getSampleSizeMeans(design3))$show())
expect_output(summary(getSimulationMeans(design3, stDev = 4, plannedSubjects = (1:3) * 200, alternative = c(1, 2)))$show())
expect_output(summary(getSimulationRates(design3,
plannedSubjects = (1:3) * 200, pi1 = c(0.3, 0.4), maxNumberOfIterations = 1000,
minNumberOfSubjectsPerStage = c(NA, 40, 40), maxNumberOfSubjectsPerStage = c(NA, 40, 400), conditionalPower = 0.8
))$show())
expect_output(summary(getSimulationMeans(getDesignGroupSequential(kMax = 1),
stDev = 4, plannedSubjects = 200, alternative = 1
))$show())
})
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