Nothing
## |
## | *Analysis of means with group sequential and combination test*
## |
## | 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 version: $Revision: 7147 $
## | Last changed: $Date: 2023-07-03 08:10:31 +0200 (Mo, 03 Jul 2023) $
## | Last changed by: $Author: pahlke $
## |
#' @include f_logger.R
NULL
.getAnalysisResultsMeans <- function(..., design, dataInput) {
if (.isTrialDesignGroupSequential(design)) {
return(.getAnalysisResultsMeansGroupSequential(
design = design,
dataInput = dataInput, ...
))
}
if (.isTrialDesignInverseNormal(design)) {
return(.getAnalysisResultsMeansInverseNormal(
design = design,
dataInput = dataInput, ...
))
}
if (.isTrialDesignFisher(design)) {
return(.getAnalysisResultsMeansFisher(
design = design,
dataInput = dataInput, ...
))
}
.stopWithWrongDesignMessage(design, inclusiveConditionalDunnett = FALSE)
}
.getAnalysisResultsMeansInverseNormal <- function(...,
design, dataInput, directionUpper = C_DIRECTION_UPPER_DEFAULT,
normalApproximation = C_NORMAL_APPROXIMATION_MEANS_DEFAULT,
equalVariances = C_EQUAL_VARIANCES_DEFAULT,
thetaH0 = C_THETA_H0_MEANS_DEFAULT, thetaH1 = NA_real_,
nPlanned = NA_real_, assumedStDev = NA_real_,
allocationRatioPlanned = C_ALLOCATION_RATIO_DEFAULT,
tolerance = C_ANALYSIS_TOLERANCE_DEFAULT) {
.assertIsTrialDesignInverseNormal(design)
stage <- .getStageFromOptionalArguments(..., dataInput = dataInput, design = design)
.warnInCaseOfUnknownArguments(
functionName = ".getAnalysisResultsMeansInverseNormal",
ignore = c(.getDesignArgumentsToIgnoreAtUnknownArgumentCheck(
design,
powerCalculationEnabled = TRUE
), "stage"), ...
)
results <- AnalysisResultsInverseNormal(design = design, dataInput = dataInput)
.getAnalysisResultsMeansAll(
results = results, design = design, dataInput = dataInput,
stage = stage, directionUpper = directionUpper, normalApproximation = normalApproximation,
equalVariances = equalVariances, thetaH0 = thetaH0, thetaH1 = thetaH1, nPlanned = nPlanned,
assumedStDev = assumedStDev, allocationRatioPlanned = allocationRatioPlanned,
tolerance = tolerance
)
return(results)
}
.getAnalysisResultsMeansGroupSequential <- function(...,
design, dataInput, directionUpper = C_DIRECTION_UPPER_DEFAULT,
normalApproximation = C_NORMAL_APPROXIMATION_MEANS_DEFAULT, equalVariances = C_EQUAL_VARIANCES_DEFAULT,
thetaH0 = C_THETA_H0_MEANS_DEFAULT, thetaH1 = NA_real_, nPlanned = NA_real_, assumedStDev = NA_real_,
allocationRatioPlanned = C_ALLOCATION_RATIO_DEFAULT,
tolerance = C_ANALYSIS_TOLERANCE_DEFAULT) {
.assertIsTrialDesignGroupSequential(design)
stage <- .getStageFromOptionalArguments(..., dataInput = dataInput, design = design)
.warnInCaseOfUnknownArguments(
functionName = ".getAnalysisResultsMeansGroupSequential",
ignore = c(.getDesignArgumentsToIgnoreAtUnknownArgumentCheck(
design,
powerCalculationEnabled = TRUE
), c("stage", "stDevH1")), ...
)
results <- AnalysisResultsGroupSequential(design = design, dataInput = dataInput)
stDevH1 <- .getOptionalArgument("stDevH1", ...)
if (!is.null(stDevH1)) {
.assertIsSingleNumber(assumedStDev, "assumedStDev", naAllowed = TRUE)
if (!is.na(assumedStDev)) {
if (!identical(assumedStDev, stDevH1)) {
stop(C_EXCEPTION_TYPE_CONFLICTING_ARGUMENTS, "either 'assumedStDev' or 'stDevH1' must be defined")
}
}
assumedStDev <- stDevH1
}
.getAnalysisResultsMeansAll(
results = results, design = design, dataInput = dataInput,
stage = stage, directionUpper = directionUpper, normalApproximation = normalApproximation,
equalVariances = equalVariances, thetaH0 = thetaH0, thetaH1 = thetaH1, nPlanned = nPlanned,
assumedStDev = assumedStDev, allocationRatioPlanned = allocationRatioPlanned,
tolerance = tolerance
)
return(results)
}
.getAnalysisResultsMeansFisher <- function(...,
design, dataInput, directionUpper = C_DIRECTION_UPPER_DEFAULT,
normalApproximation = C_NORMAL_APPROXIMATION_MEANS_DEFAULT, equalVariances = C_EQUAL_VARIANCES_DEFAULT,
thetaH0 = C_THETA_H0_MEANS_DEFAULT, thetaH1 = NA_real_, nPlanned = NA_real_, assumedStDev = NA_real_,
allocationRatioPlanned = C_ALLOCATION_RATIO_DEFAULT,
tolerance = C_ANALYSIS_TOLERANCE_DEFAULT,
iterations = C_ITERATIONS_DEFAULT, seed = NA_real_) {
.assertIsTrialDesignFisher(design)
.assertIsValidIterationsAndSeed(iterations, seed, zeroIterationsAllowed = FALSE)
stage <- .getStageFromOptionalArguments(..., dataInput = dataInput, design = design)
.warnInCaseOfUnknownArguments(
functionName = ".getAnalysisResultsMeansFisher",
ignore = c(.getDesignArgumentsToIgnoreAtUnknownArgumentCheck(
design,
powerCalculationEnabled = TRUE
), "stage"), ...
)
results <- AnalysisResultsFisher(design = design, dataInput = dataInput)
.setValueAndParameterType(results, "iterations", as.integer(iterations), C_ITERATIONS_DEFAULT)
.setValueAndParameterType(results, "seed", seed, NA_real_)
.getAnalysisResultsMeansAll(
results = results, design = design, dataInput = dataInput,
stage = stage, directionUpper = directionUpper, normalApproximation = normalApproximation,
equalVariances = equalVariances, thetaH0 = thetaH0, thetaH1 = thetaH1, nPlanned = nPlanned,
assumedStDev = assumedStDev, allocationRatioPlanned = allocationRatioPlanned,
tolerance = tolerance, iterations = iterations,
seed = seed
)
return(results)
}
#'
#' The following parameters will be taken from 'design':
#' stages, informationRates, criticalValues, futilityBounds, alphaSpent, stageLevels
#'
#' @noRd
#'
.getAnalysisResultsMeansAll <- function(..., results, design, dataInput, stage,
directionUpper, normalApproximation = normalApproximation,
equalVariances = equalVariances, thetaH0, thetaH1, assumedStDev,
nPlanned, allocationRatioPlanned, tolerance,
iterations, seed) {
startTime <- Sys.time()
.assertIsValidTolerance(tolerance)
stageResults <- .getStageResultsMeans(
design = design, dataInput = dataInput, stage = stage,
thetaH0 = thetaH0, directionUpper = directionUpper,
normalApproximation = normalApproximation, equalVariances = equalVariances
)
results$.setStageResults(stageResults)
.logProgress("Stage results calculated", startTime = startTime)
assumedStDev <- .assertIsValidAssumedStDev(assumedStDev, stageResults, stage, results = results)
thetaH1 <- .assertIsValidThetaH1(thetaH1, stageResults, stage, results = results)
.setValueAndParameterType(results, "thetaH0", thetaH0, C_THETA_H0_MEANS_DEFAULT)
.setValueAndParameterType(results, "directionUpper", directionUpper, C_DIRECTION_UPPER_DEFAULT)
.setValueAndParameterType(
results, "normalApproximation",
normalApproximation, C_NORMAL_APPROXIMATION_MEANS_DEFAULT
)
if (stageResults$isTwoSampleDataset()) {
.setValueAndParameterType(results, "equalVariances", equalVariances, C_EQUAL_VARIANCES_DEFAULT)
} else {
results$.setParameterType("equalVariances", C_PARAM_NOT_APPLICABLE)
}
.setConditionalPowerArguments(results, dataInput, nPlanned, allocationRatioPlanned)
.setNPlannedAndThetaH1AndAssumedStDev(results, nPlanned, thetaH1, assumedStDev)
# test actions
results$testActions <- getTestActions(stageResults = stageResults)
results$.setParameterType("testActions", C_PARAM_GENERATED)
if (design$kMax > 1) {
# conditional power
startTime <- Sys.time()
if (.isTrialDesignFisher(design)) {
results$.conditionalPowerResults <- .getConditionalPowerMeans(
stageResults = stageResults,
nPlanned = nPlanned, allocationRatioPlanned = allocationRatioPlanned,
assumedStDev = assumedStDev, thetaH1 = thetaH1,
iterations = iterations, seed = seed
)
.synchronizeIterationsAndSeed(results)
} else {
results$.conditionalPowerResults <- .getConditionalPowerMeans(
stageResults = stageResults,
nPlanned = nPlanned, allocationRatioPlanned = allocationRatioPlanned,
assumedStDev = assumedStDev, thetaH1 = thetaH1
)
results$conditionalPower <- results$.conditionalPowerResults$conditionalPower
results$.setParameterType("conditionalPower", C_PARAM_GENERATED)
}
.logProgress("Conditional power calculated", startTime = startTime)
# CRP - conditional rejection probabilities
startTime <- Sys.time()
if (.isTrialDesignFisher(design) && isTRUE(.getOptionalArgument("simulateCRP", ...))) {
results$.setParameterType("seed", ifelse(is.na(seed), C_PARAM_DEFAULT_VALUE, C_PARAM_USER_DEFINED))
seed <- results$.conditionalPowerResults$seed
crp <- getConditionalRejectionProbabilities(
stageResults = stageResults, iterations = iterations, seed = seed
)
results$conditionalRejectionProbabilities <- crp$crpFisherSimulated
paramTypeSeed <- results$.conditionalPowerResults$.getParameterType("seed")
if (paramTypeSeed != C_PARAM_TYPE_UNKNOWN) {
results$.setParameterType("seed", paramTypeSeed)
}
results$seed <- seed
} else {
results$conditionalRejectionProbabilities <-
getConditionalRejectionProbabilities(stageResults = stageResults)
}
results$.setParameterType("conditionalRejectionProbabilities", C_PARAM_GENERATED)
.logProgress("Conditional rejection probabilities (CRP) calculated", startTime = startTime)
}
# RCI - repeated confidence interval
startTime <- Sys.time()
repeatedConfidenceIntervals <- .getRepeatedConfidenceIntervalsMeans(
design = design, dataInput = dataInput, stage = stage,
normalApproximation = normalApproximation, equalVariances = equalVariances,
tolerance = tolerance
)
results$repeatedConfidenceIntervalLowerBounds <- repeatedConfidenceIntervals[1, ]
results$repeatedConfidenceIntervalUpperBounds <- repeatedConfidenceIntervals[2, ]
.logProgress("Repeated confidence interval calculated", startTime = startTime)
# repeated p-value
startTime <- Sys.time()
results$repeatedPValues <- getRepeatedPValues(
stageResults = stageResults, tolerance = tolerance
)
.logProgress("Repeated p-values calculated", startTime = startTime)
results$.setParameterType("repeatedConfidenceIntervalLowerBounds", C_PARAM_GENERATED)
results$.setParameterType("repeatedConfidenceIntervalUpperBounds", C_PARAM_GENERATED)
results$.setParameterType("repeatedPValues", C_PARAM_GENERATED)
if (design$kMax > 1) {
startTime <- Sys.time()
# final p-value
finalPValue <- getFinalPValue(stageResults, showWarnings = FALSE)
results$finalPValues <- .getVectorWithFinalValueAtFinalStage(
kMax = design$kMax,
finalValue = finalPValue$pFinal, finalStage = finalPValue$finalStage
)
results$finalStage <- finalPValue$finalStage
results$.setParameterType("finalPValues", C_PARAM_GENERATED)
results$.setParameterType("finalStage", C_PARAM_GENERATED)
.logProgress("Final p-value calculated", startTime = startTime)
# final confidence interval & median unbiased estimate
startTime <- Sys.time()
finalConfidenceIntervals <- .getFinalConfidenceIntervalMeans(
design = design, dataInput = dataInput,
thetaH0 = thetaH0, stage = stage, directionUpper = directionUpper,
normalApproximation = normalApproximation,
equalVariances = equalVariances, tolerance = tolerance
)
if (!is.null(finalConfidenceIntervals)) {
finalStage <- finalConfidenceIntervals$finalStage
results$finalConfidenceIntervalLowerBounds <- .getVectorWithFinalValueAtFinalStage(
kMax = design$kMax,
finalValue = finalConfidenceIntervals$finalConfidenceInterval[1], finalStage = finalStage
)
results$finalConfidenceIntervalUpperBounds <- .getVectorWithFinalValueAtFinalStage(
kMax = design$kMax,
finalValue = finalConfidenceIntervals$finalConfidenceInterval[2], finalStage = finalStage
)
results$medianUnbiasedEstimates <- .getVectorWithFinalValueAtFinalStage(
kMax = design$kMax,
finalValue = finalConfidenceIntervals$medianUnbiased, finalStage = finalStage
)
results$.setParameterType("finalConfidenceIntervalLowerBounds", C_PARAM_GENERATED)
results$.setParameterType("finalConfidenceIntervalUpperBounds", C_PARAM_GENERATED)
results$.setParameterType("medianUnbiasedEstimates", C_PARAM_GENERATED)
.logProgress("Final confidence interval calculated", startTime = startTime)
}
}
return(results)
}
.getStageResultsMeans <- function(..., design, dataInput,
thetaH0 = C_THETA_H0_MEANS_DEFAULT,
directionUpper = C_DIRECTION_UPPER_DEFAULT,
normalApproximation = C_NORMAL_APPROXIMATION_MEANS_DEFAULT,
equalVariances = C_EQUAL_VARIANCES_DEFAULT,
stage = NA_integer_, userFunctionCallEnabled = FALSE) {
.assertIsDatasetMeans(dataInput = dataInput)
.assertIsValidThetaH0DataInput(thetaH0, dataInput)
.assertIsValidDirectionUpper(directionUpper, design$sided,
userFunctionCallEnabled = userFunctionCallEnabled
)
.assertIsSingleLogical(normalApproximation, "normalApproximation")
.assertIsSingleLogical(equalVariances, "equalVariances")
.warnInCaseOfUnknownArguments(
functionName = "getStageResultsMeans",
ignore = .getDesignArgumentsToIgnoreAtUnknownArgumentCheck(
design,
powerCalculationEnabled = TRUE
), ...
)
stage <- .getStageFromOptionalArguments(...,
dataInput = dataInput,
design = design, stage = stage
)
effectSizes <- rep(NA_real_, design$kMax)
if (dataInput$getNumberOfGroups() == 1) {
overallTestStatistics <- c((dataInput$getOverallMeansUpTo(stage) - thetaH0) /
dataInput$getOverallStDevsUpTo(stage) *
sqrt(dataInput$getOverallSampleSizesUpTo(stage)), rep(NA_real_, design$kMax - stage))
if (normalApproximation) {
overallPValues <- 1 - stats::pnorm(overallTestStatistics)
} else {
overallPValues <- 1 - stats::pt(
overallTestStatistics,
dataInput$getOverallSampleSizesUpTo(stage) - 1
)
}
effectSizes[1:stage] <- dataInput$getOverallMeansUpTo(stage)
}
if (dataInput$getNumberOfGroups() == 2) {
# common variance
overallStDevs <- rep(NA_real_, design$kMax)
for (k in 1:stage) {
overallStDevs[k] <- sqrt(((sum(dataInput$getSampleSizesUpTo(k, 1)) - 1) *
dataInput$getOverallStDev(k)^2 +
(sum(dataInput$getSampleSizesUpTo(k, 2)) - 1) * dataInput$getOverallStDev(k, 2)^2) /
(sum(dataInput$getSampleSizesUpTo(k, 1)) + sum(dataInput$getSampleSizesUpTo(k, 2)) - 2))
}
overallSampleSizes1 <- dataInput$getOverallSampleSizesUpTo(stage)
overallSampleSizes2 <- dataInput$getOverallSampleSizesUpTo(stage, 2)
if (equalVariances) {
overallTestStatistics <- c(
(dataInput$getOverallMeansUpTo(stage) -
dataInput$getOverallMeansUpTo(stage, 2) - thetaH0) /
overallStDevs[1:stage] /
sqrt(1 / overallSampleSizes1 + 1 / overallSampleSizes2),
rep(NA_real_, design$kMax - stage)
)
} else {
overallTestStatistics <- c(
(dataInput$getOverallMeansUpTo(stage) -
dataInput$getOverallMeansUpTo(stage, 2) - thetaH0) /
(sqrt(dataInput$getOverallStDevsUpTo(stage)^2 / overallSampleSizes1 +
dataInput$getOverallStDevsUpTo(stage, 2)^2 / overallSampleSizes2)),
rep(NA_real_, design$kMax - stage)
)
}
if (normalApproximation) {
overallPValues <- 1 - stats::pnorm(overallTestStatistics)
} else {
if (equalVariances) {
overallPValues <- 1 - stats::pt(
overallTestStatistics,
overallSampleSizes1 + overallSampleSizes2 - 2
)
} else {
u <- dataInput$getOverallStDevsUpTo(stage)^2 / overallSampleSizes1 /
(dataInput$getOverallStDevsUpTo(stage)^2 / overallSampleSizes1 +
dataInput$getOverallStDevsUpTo(stage, 2)^2 / overallSampleSizes2)
overallPValues <- 1 - stats::pt(
overallTestStatistics,
1 / (u^2 / (overallSampleSizes1 - 1) +
(1 - u)^2 / (overallSampleSizes2 - 1))
)
}
}
effectSizes[1:stage] <- dataInput$getOverallMeansUpTo(stage) - dataInput$getOverallMeansUpTo(stage, 2)
}
if (!directionUpper) {
overallPValues <- 1 - overallPValues
}
# calculation of stage-wise test statistics and combination tests
testStatistics <- rep(NA_real_, design$kMax)
pValues <- rep(NA_real_, design$kMax)
combInverseNormal <- rep(NA_real_, design$kMax)
combFisher <- rep(NA_real_, design$kMax)
weightsInverseNormal <- .getWeightsInverseNormal(design)
weightsFisher <- .getWeightsFisher(design)
for (k in 1:stage) {
if (dataInput$getNumberOfGroups() == 1) {
# stage-wise test statistics
testStatistics[k] <- (dataInput$getMean(k) - thetaH0) /
dataInput$getStDev(k) * sqrt(dataInput$getSampleSize(k))
if (normalApproximation) {
# stage-wise p-values
pValues[k] <- 1 - stats::pnorm(testStatistics[k])
} else {
pValues[k] <- 1 - stats::pt(testStatistics[k], dataInput$getSampleSize(k) - 1)
}
}
if (dataInput$getNumberOfGroups() == 2) {
# stage-wise test statistics
if (equalVariances) {
testStatistics[k] <- (dataInput$getMean(k, 1) - dataInput$getMean(k, 2) - thetaH0) /
sqrt(((dataInput$getSampleSize(k, 1) - 1) * dataInput$getStDev(k, 1)^2 +
(dataInput$getSampleSize(k, 2) - 1) * dataInput$getStDev(k, 2)^2) /
(dataInput$getSampleSize(k, 1) + dataInput$getSampleSize(k, 2) - 2)) /
sqrt(1 / dataInput$getSampleSize(k, 1) + 1 / dataInput$getSampleSize(k, 2))
} else {
testStatistics[k] <- (dataInput$getMean(k, 1) - dataInput$getMean(k, 2) - thetaH0) /
sqrt(dataInput$getStDev(k, 1)^2 / dataInput$getSampleSize(k, 1) +
dataInput$getStDev(k, 2)^2 / dataInput$getSampleSize(k, 2))
}
if (normalApproximation) {
# stage-wise p-values
pValues[k] <- 1 - stats::pnorm(testStatistics[k])
} else {
if (equalVariances) {
pValues[k] <- 1 - stats::pt(
testStatistics[k],
dataInput$getSampleSize(k, 1) + dataInput$getSampleSize(k, 2) - 2
)
} else {
u <- dataInput$getStDev(k, 1)^2 / dataInput$getSampleSize(k, 1) / (dataInput$getStDev(k, 1)^2 /
dataInput$getSampleSize(k, 1) + dataInput$getStDev(k, 2)^2 / dataInput$getSampleSize(k, 2))
pValues[k] <- 1 - stats::pt(
testStatistics[k],
1 / (u^2 / (dataInput$getSampleSize(k, 1) - 1) +
(1 - u)^2 / (dataInput$getSampleSize(k, 2) - 1))
)
}
}
}
if (!directionUpper) {
pValues[k] <- 1 - pValues[k]
}
# inverse normal test
combInverseNormal[k] <- (weightsInverseNormal[1:k] %*% .getOneMinusQNorm(pValues[1:k])) /
sqrt(sum(weightsInverseNormal[1:k]^2))
# Fisher combination test
combFisher[k] <- prod(pValues[1:k]^weightsFisher[1:k])
}
if (dataInput$getNumberOfGroups() == 1) {
stageResults <- StageResultsMeans(
design = design,
dataInput = dataInput,
stage = as.integer(stage),
overallTestStatistics = .fillWithNAs(overallTestStatistics, design$kMax),
overallPValues = .fillWithNAs(overallPValues, design$kMax),
overallMeans = .trimAnalysisMeansResultObjectAndFillWithNAs(
dataInput$getOverallMeans(), design$kMax
),
overallStDevs = .trimAnalysisMeansResultObjectAndFillWithNAs(
dataInput$getOverallStDevs(), design$kMax
),
overallSampleSizes = .fillWithNAs(dataInput$getOverallSampleSizesUpTo(stage), design$kMax),
testStatistics = testStatistics,
effectSizes = effectSizes,
pValues = pValues,
combInverseNormal = combInverseNormal,
combFisher = combFisher,
weightsFisher = weightsFisher,
weightsInverseNormal = weightsInverseNormal,
thetaH0 = thetaH0,
direction = ifelse(directionUpper, C_DIRECTION_UPPER, C_DIRECTION_LOWER),
normalApproximation = normalApproximation,
equalVariances = equalVariances
)
} else if (dataInput$getNumberOfGroups() == 2) {
stageResults <- StageResultsMeans(
design = design,
dataInput = dataInput,
stage = as.integer(stage),
overallTestStatistics = .fillWithNAs(overallTestStatistics, design$kMax),
overallPValues = .fillWithNAs(overallPValues, design$kMax),
overallMeans1 = .trimAnalysisMeansResultObjectAndFillWithNAs(
dataInput$getOverallMeans(group = 1), design$kMax
),
overallMeans2 = .trimAnalysisMeansResultObjectAndFillWithNAs(
dataInput$getOverallMeans(group = 2), design$kMax
),
overallStDevs1 = .trimAnalysisMeansResultObjectAndFillWithNAs(
dataInput$getOverallStDevs(group = 1), design$kMax
),
overallStDevs2 = .trimAnalysisMeansResultObjectAndFillWithNAs(
dataInput$getOverallStDevs(group = 2), design$kMax
),
overallStDevs = overallStDevs, # common variance
overallSampleSizes1 = .fillWithNAs(dataInput$getOverallSampleSizesUpTo(stage), design$kMax),
overallSampleSizes2 = .fillWithNAs(dataInput$getOverallSampleSizesUpTo(stage, 2), design$kMax),
effectSizes = effectSizes,
testStatistics = testStatistics,
pValues = pValues,
combInverseNormal = combInverseNormal,
combFisher = combFisher,
weightsFisher = weightsFisher,
weightsInverseNormal = weightsInverseNormal,
thetaH0 = thetaH0,
direction = ifelse(directionUpper, C_DIRECTION_UPPER, C_DIRECTION_LOWER),
normalApproximation = normalApproximation,
equalVariances = equalVariances
)
}
if (.isTrialDesignFisher(design)) {
stageResults$.setParameterType("combFisher", C_PARAM_GENERATED)
stageResults$.setParameterType("weightsFisher", C_PARAM_GENERATED)
} else if (.isTrialDesignInverseNormal(design)) {
stageResults$.setParameterType("combInverseNormal", C_PARAM_GENERATED)
stageResults$.setParameterType("weightsInverseNormal", C_PARAM_GENERATED)
}
return(stageResults)
}
.trimAnalysisMeansResultObjectAndFillWithNAs <- function(x, kMax) {
return(.fillWithNAs(.trimAnalysisMeansResultObject(x, kMax), kMax))
}
.trimAnalysisMeansResultObject <- function(x, kMax) {
if (is.matrix(x)) {
if (ncol(x) <= kMax) {
return(x)
}
return(x[, 1:kMax])
}
if (length(x) <= kMax) {
return(x)
}
return(x[1:kMax])
}
#'
#' Calculation of lower and upper limits of repeated confidence intervals (RCIs) for Means
#'
#' @noRd
#'
.getRepeatedConfidenceIntervalsMeans <- function(design, ...) {
if (.isTrialDesignGroupSequential(design)) {
return(.getRepeatedConfidenceIntervalsMeansGroupSequential(design = design, ...))
}
if (.isTrialDesignInverseNormal(design)) {
return(.getRepeatedConfidenceIntervalsMeansInverseNormal(design = design, ...))
}
if (.isTrialDesignFisher(design)) {
return(.getRepeatedConfidenceIntervalsMeansFisher(design = design, ...))
}
.stopWithWrongDesignMessage(design, inclusiveConditionalDunnett = FALSE)
}
.getRootThetaMeans <- function(..., design, dataInput, stage,
directionUpper, normalApproximation = normalApproximation, equalVariances = equalVariances,
thetaLow, thetaUp, firstParameterName, secondValue, tolerance,
callingFunctionInformation = NA_character_) {
result <- .getOneDimensionalRoot(
function(theta) {
stageResults <- .getStageResultsMeans(
design = design, dataInput = dataInput,
stage = stage, thetaH0 = theta, directionUpper = directionUpper,
normalApproximation = normalApproximation, equalVariances = equalVariances
)
firstValue <- stageResults[[firstParameterName]][stage]
if (.isTrialDesignGroupSequential(design)) {
firstValue <- .getOneMinusQNorm(firstValue)
}
return(firstValue - secondValue)
},
lower = thetaLow, upper = thetaUp, tolerance = tolerance,
callingFunctionInformation = callingFunctionInformation
)
return(result)
}
.getUpperLowerThetaMeans <- function(..., design, dataInput, theta, stage,
directionUpper, normalApproximation = normalApproximation,
equalVariances = equalVariances, conditionFunction,
firstParameterName, secondValue) {
stageResults <- .getStageResultsMeans(
design = design, dataInput = dataInput,
stage = stage, thetaH0 = theta, directionUpper = directionUpper,
normalApproximation = normalApproximation, equalVariances = equalVariances
)
firstValue <- stageResults[[firstParameterName]][stage]
if (.isTrialDesignGroupSequential(design)) {
firstValue <- .getOneMinusQNorm(firstValue)
}
maxSearchIterations <- 50
while (conditionFunction(secondValue, firstValue)) {
theta <- 2 * theta
stageResults <- .getStageResultsMeans(
design = design, dataInput = dataInput,
stage = stage, thetaH0 = theta, directionUpper = directionUpper,
normalApproximation = normalApproximation, equalVariances = equalVariances
)
firstValue <- stageResults[[firstParameterName]][stage]
if (.isTrialDesignGroupSequential(design)) {
firstValue <- .getOneMinusQNorm(firstValue)
}
maxSearchIterations <- maxSearchIterations - 1
if (maxSearchIterations < 0) {
stop(sprintf(
paste0(
"Failed to find theta (k = %s, firstValue = %s, ",
"secondValue = %s, levels(firstValue) = %s, theta = %s)"
),
stage, stageResults[[firstParameterName]][stage], secondValue,
firstValue, theta
))
}
}
return(theta)
}
.getRepeatedConfidenceIntervalsMeansAll <- function(...,
design, dataInput,
normalApproximation = C_NORMAL_APPROXIMATION_MEANS_DEFAULT,
equalVariances = C_EQUAL_VARIANCES_DEFAULT,
directionUpper = C_DIRECTION_UPPER_DEFAULT,
tolerance = C_ANALYSIS_TOLERANCE_DEFAULT,
firstParameterName) {
stage <- .getStageFromOptionalArguments(..., dataInput = dataInput, design = design)
futilityCorr <- rep(NA_real_, design$kMax) # necessary for adjustment for binding futility boundaries
criticalValues <- design$criticalValues
criticalValues[is.infinite(criticalValues) & criticalValues > 0] <- C_QNORM_MAXIMUM
criticalValues[is.infinite(criticalValues) & criticalValues < 0] <- C_QNORM_MINIMUM
if (.isTrialDesignFisher(design)) {
bounds <- design$alpha0Vec
border <- C_ALPHA_0_VEC_DEFAULT
conditionFunction <- .isFirstValueSmallerThanSecondValue
} else {
bounds <- design$futilityBounds
border <- C_FUTILITY_BOUNDS_DEFAULT
conditionFunction <- .isFirstValueGreaterThanSecondValue
}
repeatedConfidenceIntervals <- matrix(NA_real_, nrow = 2, ncol = design$kMax)
for (k in 1:stage) {
startTime <- Sys.time()
if (criticalValues[k] < C_QNORM_MAXIMUM) {
# finding maximum upper and minimum lower bounds for RCIs
thetaLow <- .getUpperLowerThetaMeans(
design = design, dataInput = dataInput,
theta = -1, stage = k, directionUpper = TRUE,
normalApproximation = normalApproximation, equalVariances = equalVariances,
conditionFunction = conditionFunction,
firstParameterName = firstParameterName, secondValue = criticalValues[k]
)
thetaUp <- .getUpperLowerThetaMeans(
design = design, dataInput = dataInput,
theta = 1, stage = k, directionUpper = FALSE,
normalApproximation = normalApproximation, equalVariances = equalVariances,
conditionFunction = conditionFunction,
firstParameterName = firstParameterName, secondValue = criticalValues[k]
)
# finding upper and lower RCI limits through root function
repeatedConfidenceIntervals[1, k] <- .getRootThetaMeans(
design = design, dataInput = dataInput, stage = k,
directionUpper = TRUE, normalApproximation = normalApproximation,
equalVariances = equalVariances, thetaLow = thetaLow, thetaUp = thetaUp,
firstParameterName = firstParameterName, secondValue = criticalValues[k], tolerance = tolerance,
callingFunctionInformation = paste0("Repeated confidence interval [1, ", k, "]")
)
repeatedConfidenceIntervals[2, k] <- .getRootThetaMeans(
design = design, dataInput = dataInput, stage = k,
directionUpper = FALSE, normalApproximation = normalApproximation,
equalVariances = equalVariances, thetaLow = thetaLow, thetaUp = thetaUp,
firstParameterName = firstParameterName, secondValue = criticalValues[k], tolerance = tolerance,
callingFunctionInformation = paste0("Repeated confidence interval [2, ", k, "]")
)
# adjustment for binding futility bounds
if (k > 1 && !is.na(bounds[k - 1]) && conditionFunction(bounds[k - 1], border) && design$bindingFutility) {
parameterName <- ifelse(.isTrialDesignFisher(design), "pValues", firstParameterName)
# Calculate new lower and upper bounds
if (directionUpper) {
thetaLow <- .getUpperLowerThetaMeans(
design = design, dataInput = dataInput, theta = -1, stage = k - 1,
directionUpper = TRUE, normalApproximation = normalApproximation,
equalVariances = equalVariances, conditionFunction = conditionFunction,
firstParameterName = parameterName, secondValue = bounds[k - 1]
)
} else {
thetaUp <- .getUpperLowerThetaMeans(
design = design, dataInput = dataInput, theta = 1, stage = k - 1,
directionUpper = FALSE, normalApproximation = normalApproximation,
equalVariances = equalVariances, conditionFunction = conditionFunction,
firstParameterName = parameterName, secondValue = bounds[k - 1]
)
}
futilityCorr[k] <- .getRootThetaMeans(
design = design, dataInput = dataInput, stage = k - 1,
directionUpper = directionUpper, normalApproximation = normalApproximation,
equalVariances = equalVariances, thetaLow = thetaLow, thetaUp = thetaUp,
firstParameterName = parameterName, secondValue = bounds[k - 1],
tolerance = tolerance, callingFunctionInformation =
paste0("Repeated confidence interval, futility correction [", k, "]")
)
if (directionUpper) {
repeatedConfidenceIntervals[1, k] <- min(min(futilityCorr[2:k]), repeatedConfidenceIntervals[1, k])
} else {
repeatedConfidenceIntervals[2, k] <- max(max(futilityCorr[2:k]), repeatedConfidenceIntervals[2, k])
}
}
if (!is.na(repeatedConfidenceIntervals[1, k]) && !is.na(repeatedConfidenceIntervals[2, k]) &&
repeatedConfidenceIntervals[1, k] > repeatedConfidenceIntervals[2, k]) {
repeatedConfidenceIntervals[, k] <- rep(NA_real_, 2)
}
}
.logProgress("Repeated confidence interval of stage %s calculated", startTime = startTime, k)
}
return(repeatedConfidenceIntervals)
}
#'
#' RCIs based on group sequential combination test
#'
#' @noRd
#'
.getRepeatedConfidenceIntervalsMeansGroupSequential <- function(...,
design, dataInput,
normalApproximation = C_NORMAL_APPROXIMATION_MEANS_DEFAULT,
equalVariances = C_EQUAL_VARIANCES_DEFAULT,
directionUpper = C_DIRECTION_UPPER_DEFAULT,
tolerance = C_ANALYSIS_TOLERANCE_DEFAULT) {
.warnInCaseOfUnknownArguments(
functionName =
".getRepeatedConfidenceIntervalsMeansGroupSequential",
ignore = c(.getDesignArgumentsToIgnoreAtUnknownArgumentCheck(
design,
powerCalculationEnabled = TRUE
), "stage"), ...
)
return(.getRepeatedConfidenceIntervalsMeansAll(
design = design, dataInput = dataInput,
normalApproximation = normalApproximation, equalVariances = equalVariances,
directionUpper = directionUpper, tolerance = tolerance, firstParameterName = "overallPValues", ...
))
}
#'
#' RCIs based on inverse normal combination test
#'
#' @noRd
#'
.getRepeatedConfidenceIntervalsMeansInverseNormal <- function(...,
design, dataInput,
normalApproximation = C_NORMAL_APPROXIMATION_MEANS_DEFAULT,
equalVariances = C_EQUAL_VARIANCES_DEFAULT,
directionUpper = C_DIRECTION_UPPER_DEFAULT,
tolerance = C_ANALYSIS_TOLERANCE_DEFAULT) {
.warnInCaseOfUnknownArguments(
functionName =
".getRepeatedConfidenceIntervalsMeansInverseNormal",
ignore = c(.getDesignArgumentsToIgnoreAtUnknownArgumentCheck(
design,
powerCalculationEnabled = TRUE
), "stage"), ...
)
return(.getRepeatedConfidenceIntervalsMeansAll(
design = design, dataInput = dataInput,
normalApproximation = normalApproximation, equalVariances = equalVariances,
directionUpper = directionUpper, tolerance = tolerance,
firstParameterName = "combInverseNormal", ...
))
}
#'
#' RCIs based on Fisher's combination test
#'
#' @noRd
#'
.getRepeatedConfidenceIntervalsMeansFisher <- function(...,
design, dataInput,
normalApproximation = C_NORMAL_APPROXIMATION_MEANS_DEFAULT,
equalVariances = C_EQUAL_VARIANCES_DEFAULT,
directionUpper = C_DIRECTION_UPPER_DEFAULT,
tolerance = C_ANALYSIS_TOLERANCE_DEFAULT) {
.warnInCaseOfUnknownArguments(
functionName =
".getRepeatedConfidenceIntervalsMeansFisher",
ignore = c(.getDesignArgumentsToIgnoreAtUnknownArgumentCheck(
design,
powerCalculationEnabled = TRUE
), "stage"), ...
)
return(.getRepeatedConfidenceIntervalsMeansAll(
design = design, dataInput = dataInput,
normalApproximation = normalApproximation, equalVariances = equalVariances,
directionUpper = directionUpper, tolerance = tolerance, firstParameterName = "combFisher", ...
))
}
#'
#' Calculation of conditional power based on group sequential method
#'
#' @noRd
#'
.getConditionalPowerMeansGroupSequential <- function(..., stageResults, stage = stageResults$stage,
allocationRatioPlanned = C_ALLOCATION_RATIO_DEFAULT, nPlanned = NA_real_,
thetaH1 = NA_real_, assumedStDev = NA_real_) {
design <- stageResults$.design
.assertIsTrialDesignGroupSequential(design)
.assertIsValidStage(stage, design$kMax)
assumedStDev <- .assertIsValidAssumedStDev(assumedStDev, stageResults, stage)
thetaH1 <- .assertIsValidThetaH1(thetaH1, stageResults, stage)
.warnInCaseOfUnknownArguments(
functionName = ".getConditionalPowerMeansGroupSequential",
ignore = c("stage", "design", "stageResultsName", "grid", "stDevH1"), ...
)
kMax <- design$kMax
conditionalPower <- rep(NA_real_, kMax)
weights <- stageResults$weightsInverseNormal
informationRates <- design$informationRates
nPlanned <- c(rep(NA, stage), nPlanned)
if (stage == kMax) {
.logDebug(
"Conditional power will be calculated only for subsequent stages ",
"(stage = ", stage, ", kMax = ", design$kMax, ")"
)
return(list(
nPlanned = nPlanned,
conditionalPower = conditionalPower
))
}
criticalValues <- design$criticalValues
if (stageResults$isTwoSampleDataset()) {
.assertIsSingleNumber(allocationRatioPlanned, "allocationRatioPlanned")
.assertIsInOpenInterval(allocationRatioPlanned, "allocationRatioPlanned", 0, C_ALLOCATION_RATIO_MAXIMUM)
nPlanned <- allocationRatioPlanned / (1 + allocationRatioPlanned)^2 * nPlanned
}
if (stageResults$direction == "upper") {
thetaH1 <- (thetaH1 - stageResults$thetaH0) / assumedStDev
} else {
thetaH1 <- -(thetaH1 - stageResults$thetaH0) / assumedStDev
}
# shifted decision region for use in getGroupSeqProbs
# Group Sequential Method
shiftedDecisionRegionUpper <- criticalValues[(stage + 1):kMax] *
sqrt(sum(weights[1:stage]^2) + cumsum(weights[(stage + 1):kMax]^2)) /
sqrt(cumsum(weights[(stage + 1):kMax]^2)) -
.getOneMinusQNorm(stageResults$overallPValues[stage]) * sqrt(sum(weights[1:stage]^2)) /
sqrt(cumsum(weights[(stage + 1):kMax]^2)) -
thetaH1 * cumsum(sqrt(nPlanned[(stage + 1):kMax]) * weights[(stage + 1):kMax]) /
sqrt(cumsum(weights[(stage + 1):kMax]^2))
if (design$sided == 2) {
shiftedDecisionRegionLower <- -criticalValues[(stage + 1):kMax] *
sqrt(sum(weights[1:stage]^2) + cumsum(weights[(stage + 1):kMax]^2)) /
sqrt(cumsum(weights[(stage + 1):kMax]^2)) -
c(weights[1:stage] %*% .getOneMinusQNorm(stageResults$pValues[1:stage])) /
sqrt(cumsum(weights[(stage + 1):kMax]^2)) -
thetaH1 * cumsum(sqrt(nPlanned[(stage + 1):kMax]) * weights[(stage + 1):kMax]) /
sqrt(cumsum(weights[(stage + 1):kMax]^2))
}
if (stage == kMax - 1) {
shiftedFutilityBounds <- c()
} else {
shiftedFutilityBounds <- design$futilityBounds[(stage + 1):(kMax - 1)] *
sqrt(sum(weights[1:stage]^2) + cumsum(weights[(stage + 1):(kMax - 1)]^2)) /
sqrt(cumsum(weights[(stage + 1):(kMax - 1)]^2)) -
.getOneMinusQNorm(stageResults$overallPValues[stage]) * sqrt(sum(weights[1:stage]^2)) /
sqrt(cumsum(weights[(stage + 1):(kMax - 1)]^2)) -
thetaH1 * cumsum(sqrt(nPlanned[(stage + 1):(kMax - 1)]) * weights[(stage + 1):(kMax - 1)]) /
sqrt(cumsum(weights[(stage + 1):(kMax - 1)]^2))
}
# scaled information for use in getGroupSeqProbs
scaledInformation <- (informationRates[(stage + 1):kMax] - informationRates[stage]) /
(1 - informationRates[stage])
if (design$sided == 2) {
decisionMatrix <- matrix(c(shiftedDecisionRegionLower, shiftedDecisionRegionUpper), nrow = 2, byrow = TRUE)
} else {
decisionMatrix <- matrix(c(
shiftedFutilityBounds, C_FUTILITY_BOUNDS_DEFAULT,
shiftedDecisionRegionUpper
), nrow = 2, byrow = TRUE)
}
probs <- .getGroupSequentialProbabilities(
decisionMatrix = decisionMatrix,
informationRates = scaledInformation
)
if (design$twoSidedPower) {
conditionalPower[(stage + 1):kMax] <- cumsum(probs[3, ] - probs[2, ] + probs[1, ])
} else {
conditionalPower[(stage + 1):kMax] <- cumsum(probs[3, ] - probs[2, ])
}
if (stageResults$isTwoSampleDataset()) {
nPlanned <- (1 + allocationRatioPlanned)^2 / allocationRatioPlanned * nPlanned
}
return(list(
nPlanned = nPlanned,
conditionalPower = conditionalPower
))
}
#'
#' Calculation of conditional power based on inverse normal method
#'
#' @noRd
#'
.getConditionalPowerMeansInverseNormal <- function(..., stageResults, stage = stageResults$stage,
allocationRatioPlanned = C_ALLOCATION_RATIO_DEFAULT, nPlanned = NA_real_,
thetaH1 = NA_real_, assumedStDev = NA_real_) {
design <- stageResults$.design
.assertIsTrialDesignInverseNormal(design)
.assertIsValidStage(stage, design$kMax)
assumedStDev <- .assertIsValidAssumedStDev(assumedStDev, stageResults, stage)
thetaH1 <- .assertIsValidThetaH1(thetaH1, stageResults, stage)
.warnInCaseOfUnknownArguments(
functionName = ".getConditionalPowerMeansInverseNormal",
ignore = c("stage", "design", "stageResultsName", "grid", "stDevH1"), ...
)
kMax <- design$kMax
conditionalPower <- rep(NA_real_, kMax)
weights <- stageResults$weightsInverseNormal
informationRates <- design$informationRates
nPlanned <- c(rep(NA_real_, stage), nPlanned)
if (stage == kMax) {
.logDebug(
"Conditional power will be calculated only for subsequent stages ",
"(stage = ", stage, ", kMax = ", design$kMax, ")"
)
return(list(
nPlanned = nPlanned,
conditionalPower = conditionalPower
))
}
criticalValuesInverseNormal <- design$criticalValues
if (stageResults$isTwoSampleDataset()) {
.assertIsSingleNumber(allocationRatioPlanned, "allocationRatioPlanned")
.assertIsInOpenInterval(allocationRatioPlanned, "allocationRatioPlanned", 0, C_ALLOCATION_RATIO_MAXIMUM)
nPlanned <- allocationRatioPlanned / (1 + allocationRatioPlanned)^2 * nPlanned
}
if (stageResults$direction == "upper") {
thetaH1 <- (thetaH1 - stageResults$thetaH0) / assumedStDev
} else {
thetaH1 <- -(thetaH1 - stageResults$thetaH0) / assumedStDev
}
# shifted decision region for use in getGroupSeqProbs
# Inverse Normal Method
shiftedDecisionRegionUpper <- criticalValuesInverseNormal[(stage + 1):kMax] *
sqrt(sum(weights[1:stage]^2) + cumsum(weights[(stage + 1):kMax]^2)) /
sqrt(cumsum(weights[(stage + 1):kMax]^2)) -
c(weights[1:stage] %*% .getOneMinusQNorm(stageResults$pValues[1:stage])) /
sqrt(cumsum(weights[(stage + 1):kMax]^2)) -
thetaH1 * cumsum(sqrt(nPlanned[(stage + 1):kMax]) * weights[(stage + 1):kMax]) /
sqrt(cumsum(weights[(stage + 1):kMax]^2))
if (design$sided == 2) {
shiftedDecisionRegionLower <- -criticalValuesInverseNormal[(stage + 1):kMax] *
sqrt(sum(weights[1:stage]^2) + cumsum(weights[(stage + 1):kMax]^2)) /
sqrt(cumsum(weights[(stage + 1):kMax]^2)) -
c(weights[1:stage] %*% .getOneMinusQNorm(stageResults$pValues[1:stage])) /
sqrt(cumsum(weights[(stage + 1):kMax]^2)) -
thetaH1 * cumsum(sqrt(nPlanned[(stage + 1):kMax]) * weights[(stage + 1):kMax]) /
sqrt(cumsum(weights[(stage + 1):kMax]^2))
}
if (stage == kMax - 1) {
shiftedFutilityBounds <- c()
} else {
shiftedFutilityBounds <- design$futilityBounds[(stage + 1):(kMax - 1)] *
sqrt(sum(weights[1:stage]^2) + cumsum(weights[(stage + 1):(kMax - 1)]^2)) /
sqrt(cumsum(weights[(stage + 1):(kMax - 1)]^2)) -
c(weights[1:stage] %*% .getOneMinusQNorm(stageResults$pValues[1:stage])) /
sqrt(cumsum(weights[(stage + 1):(kMax - 1)]^2)) -
thetaH1 * cumsum(sqrt(nPlanned[(stage + 1):(kMax - 1)]) * weights[(stage + 1):(kMax - 1)]) /
sqrt(cumsum(weights[(stage + 1):(kMax - 1)]^2))
}
# scaled information for use in getGroupSeqProbs
scaledInformation <- (informationRates[(stage + 1):kMax] - informationRates[stage]) /
(1 - informationRates[stage])
if (design$sided == 2) {
decisionMatrix <- matrix(c(shiftedDecisionRegionLower, shiftedDecisionRegionUpper), nrow = 2, byrow = TRUE)
} else {
decisionMatrix <- matrix(c(
shiftedFutilityBounds, C_FUTILITY_BOUNDS_DEFAULT,
shiftedDecisionRegionUpper
), nrow = 2, byrow = TRUE)
}
probs <- .getGroupSequentialProbabilities(
decisionMatrix = decisionMatrix,
informationRates = scaledInformation
)
if (design$twoSidedPower) {
conditionalPower[(stage + 1):kMax] <- cumsum(probs[3, ] - probs[2, ] + probs[1, ])
} else {
conditionalPower[(stage + 1):kMax] <- cumsum(probs[3, ] - probs[2, ])
}
if (stageResults$isTwoSampleDataset()) {
nPlanned <- (1 + allocationRatioPlanned)^2 / allocationRatioPlanned * nPlanned
}
return(list(
nPlanned = nPlanned,
conditionalPower = conditionalPower
))
}
#'
#' Calculation of conditional power based on Fisher combination test
#'
#' @noRd
#'
.getConditionalPowerMeansFisher <- function(..., stageResults, stage = stageResults$stage,
allocationRatioPlanned = C_ALLOCATION_RATIO_DEFAULT, nPlanned = NA_real_,
thetaH1 = NA_real_, assumedStDev = NA_real_,
iterations = C_ITERATIONS_DEFAULT, seed = NA_real_) {
design <- stageResults$.design
.assertIsTrialDesignFisher(design)
.assertIsValidStage(stage, design$kMax)
.assertIsValidIterationsAndSeed(iterations, seed, zeroIterationsAllowed = FALSE)
assumedStDev <- .assertIsValidAssumedStDev(assumedStDev, stageResults, stage)
thetaH1 <- .assertIsValidThetaH1(thetaH1, stageResults, stage)
.warnInCaseOfUnknownArguments(
functionName = ".getConditionalPowerMeansFisher",
ignore = c("stage", "design", "stageResultsName", "grid", "stDevH1"), ...
)
kMax <- design$kMax
conditionalPower <- rep(NA_real_, kMax)
seed <- .setSeed(seed)
simulated <- FALSE
.assertIsValidNPlanned(nPlanned, kMax, stage)
nPlanned <- c(rep(NA_real_, stage), nPlanned)
if (stageResults$isTwoSampleDataset()) {
.assertIsSingleNumber(allocationRatioPlanned, "allocationRatioPlanned")
.assertIsInOpenInterval(
allocationRatioPlanned,
"allocationRatioPlanned", 0, C_ALLOCATION_RATIO_MAXIMUM
)
nPlanned <- allocationRatioPlanned / (1 + allocationRatioPlanned)^2 * nPlanned
}
if (stageResults$direction == "upper") {
thetaH1 <- (thetaH1 - stageResults$thetaH0) / assumedStDev
} else {
thetaH1 <- -(thetaH1 - stageResults$thetaH0) / assumedStDev
}
criticalValues <- design$criticalValues
weightsFisher <- stageResults$weightsFisher
pValues <- stageResults$pValues
if (stage < kMax - 1) {
for (k in (stage + 1):kMax) {
reject <- 0
for (i in 1:iterations) {
reject <- reject + .getRejectValueConditionalPowerFisher(
kMax = kMax, alpha0Vec = design$alpha0Vec,
criticalValues = criticalValues, weightsFisher = weightsFisher,
pValues = pValues, currentKMax = k, thetaH1 = thetaH1,
stage = stage, nPlanned = nPlanned
)
}
conditionalPower[k] <- reject / iterations
}
simulated <- TRUE
} else if (stage == kMax - 1) {
divisor <- prod(pValues[1:(kMax - 1)]^weightsFisher[1:(kMax - 1)])
result <- 1 - (criticalValues[kMax] / divisor)^(1 / weightsFisher[kMax])
if (result <= 0 || result >= 1) {
warning("Calculation not possible: could not calculate ",
"conditional power for stage ", kMax,
call. = FALSE
)
conditionalPower[kMax] <- NA_real_
} else {
conditionalPower[kMax] <- 1 - stats::pnorm(.getQNorm(result) - thetaH1 * sqrt(nPlanned[kMax]))
}
}
if (stageResults$isTwoSampleDataset()) {
nPlanned <- (1 + allocationRatioPlanned)^2 / allocationRatioPlanned * nPlanned
}
return(list(
nPlanned = nPlanned,
conditionalPower = conditionalPower,
iterations = as.integer(iterations),
seed = seed,
simulated = simulated
))
}
.getConditionalPowerMeans <- function(..., stageResults, nPlanned,
allocationRatioPlanned = C_ALLOCATION_RATIO_DEFAULT, thetaH1 = NA_real_, assumedStDev = NA_real_) {
stDevH1 <- .getOptionalArgument("stDevH1", ...)
if (!is.null(stDevH1) && !is.na(stDevH1)) {
if (!is.na(assumedStDev)) {
warning(sQuote("assumedStDev"), " will be ignored because ",
sQuote("stDevH1"), " is defined",
call. = FALSE
)
}
assumedStDev <- stDevH1
}
.assertIsSingleNumber(thetaH1, "thetaH1", naAllowed = TRUE)
.assertIsSingleNumber(assumedStDev, "assumedStDev", naAllowed = TRUE)
design <- stageResults$.design
results <- ConditionalPowerResultsMeans(
.stageResults = stageResults, .design = design,
nPlanned = nPlanned, allocationRatioPlanned = allocationRatioPlanned,
thetaH1 = thetaH1, assumedStDev = assumedStDev
)
if (any(is.na(nPlanned))) {
return(results)
}
if (!.isValidNPlanned(nPlanned = nPlanned, kMax = design$kMax, stage = stageResults$stage)) {
return(results)
}
if (.isTrialDesignGroupSequential(design)) {
cp <- .getConditionalPowerMeansGroupSequential(
stageResults = stageResults,
nPlanned = nPlanned, allocationRatioPlanned = allocationRatioPlanned,
thetaH1 = thetaH1, assumedStDev = assumedStDev, ...
)
} else if (.isTrialDesignInverseNormal(design)) {
cp <- .getConditionalPowerMeansInverseNormal(
stageResults = stageResults,
nPlanned = nPlanned, allocationRatioPlanned = allocationRatioPlanned,
thetaH1 = thetaH1, assumedStDev = assumedStDev, ...
)
} else if (.isTrialDesignFisher(design)) {
cp <- .getConditionalPowerMeansFisher(
stageResults = stageResults,
nPlanned = nPlanned, allocationRatioPlanned = allocationRatioPlanned,
thetaH1 = thetaH1, assumedStDev = assumedStDev, ...
)
results$iterations <- cp$iterations
results$seed <- cp$seed
results$simulated <- cp$simulated
.updateParameterTypeOfIterationsAndSeed(results, ...)
} else {
.stopWithWrongDesignMessage(design, inclusiveConditionalDunnett = FALSE)
}
results$nPlanned <- cp$nPlanned
results$conditionalPower <- cp$conditionalPower
results$.setParameterType("nPlanned", C_PARAM_GENERATED)
results$.setParameterType("conditionalPower", C_PARAM_GENERATED)
results$.setParameterType(
"allocationRatioPlanned",
ifelse(allocationRatioPlanned == C_ALLOCATION_RATIO_DEFAULT, C_PARAM_DEFAULT_VALUE, C_PARAM_USER_DEFINED)
)
results$.setParameterType("thetaH1", ifelse(is.na(thetaH1), C_PARAM_DEFAULT_VALUE, C_PARAM_USER_DEFINED))
results$.setParameterType("assumedStDev", ifelse(is.na(assumedStDev), C_PARAM_DEFAULT_VALUE, C_PARAM_USER_DEFINED))
return(results)
}
.getConditionalPowerPlotMeans <- function(..., stageResults, stage,
nPlanned, allocationRatioPlanned = C_ALLOCATION_RATIO_DEFAULT,
thetaRange, assumedStDev = NA_real_) {
.associatedArgumentsAreDefined(nPlanned = nPlanned, thetaRange = thetaRange)
.assertIsValidAllocationRatioPlanned(
allocationRatioPlanned,
stageResults$getDataInput()$getNumberOfGroups()
)
.warnInCaseOfUnknownArguments(
functionName = ".getConditionalPowerPlotMeans",
ignore = c("iterations", "seed", "stageResultsName", "grid"), ...
)
assumedStDev <- .assertIsValidAssumedStDev(assumedStDev, stageResults, stage)
thetaRange <- .assertIsValidThetaRange(thetaRange = thetaRange)
condPowerValues <- rep(NA, length(thetaRange))
likelihoodValues <- rep(NA, length(thetaRange))
if (stageResults$isOneSampleDataset()) {
stdErr <- stageResults$overallStDevs[stage] / sqrt(stageResults$overallSampleSizes[stage])
} else if (stageResults$isTwoSampleDataset()) {
stdErr <- stageResults$overallStDevs[stage] * sqrt(1 / stageResults$overallSampleSizes1[stage] + 1 /
stageResults$overallSampleSizes2[stage])
}
design <- stageResults$.design
warningMessages <- c()
withCallingHandlers(
for (i in seq(along.with = thetaRange)) {
if (.isTrialDesignGroupSequential(design)) {
condPowerValues[i] <- .getConditionalPowerMeansGroupSequential(
stageResults = stageResults, stage = stage, nPlanned = nPlanned,
allocationRatioPlanned = allocationRatioPlanned, thetaH1 = thetaRange[i],
assumedStDev = assumedStDev
)$conditionalPower[design$kMax]
} else if (.isTrialDesignInverseNormal(design)) {
condPowerValues[i] <- .getConditionalPowerMeansInverseNormal(
stageResults = stageResults, stage = stage, nPlanned = nPlanned,
allocationRatioPlanned = allocationRatioPlanned, thetaH1 = thetaRange[i],
assumedStDev = assumedStDev
)$conditionalPower[design$kMax]
} else if (.isTrialDesignFisher(design)) {
condPowerValues[i] <- .getConditionalPowerMeansFisher(
stageResults = stageResults, stage = stage, nPlanned = nPlanned,
allocationRatioPlanned = allocationRatioPlanned, thetaH1 = thetaRange[i],
assumedStDev = assumedStDev
)$conditionalPower[design$kMax]
}
likelihoodValues[i] <- stats::dnorm(
thetaRange[i],
stageResults$effectSizes[stage], stdErr
) / stats::dnorm(0, 0, stdErr)
},
warning = function(w) {
m <- w$message
if (!(m %in% warningMessages)) {
warningMessages <<- c(warningMessages, m)
}
invokeRestart("muffleWarning")
},
error = function(e) {
e
}
)
if (length(warningMessages) > 0) {
for (m in warningMessages) {
warning(m, call. = FALSE)
}
}
if (stageResults$isOneSampleDataset()) {
subtitle <- paste0(
"Stage = ", stage, ", # of remaining subjects = ",
sum(nPlanned), ", sd = ", .formatSubTitleValue(assumedStDev, "assumedStDev")
)
} else {
subtitle <- paste0(
"Stage = ", stage, ", # of remaining subjects = ",
sum(nPlanned), ", sd = ", .formatSubTitleValue(assumedStDev, "assumedStDev"),
", allocation ratio = ", .formatSubTitleValue(allocationRatioPlanned, "allocationRatioPlanned")
)
}
return(list(
xValues = thetaRange,
condPowerValues = condPowerValues,
likelihoodValues = likelihoodValues,
main = C_PLOT_MAIN_CONDITIONAL_POWER_WITH_LIKELIHOOD,
xlab = "Effect size",
ylab = C_PLOT_YLAB_CONDITIONAL_POWER_WITH_LIKELIHOOD,
sub = subtitle
))
}
#'
#' Calculation of final confidence interval
#' based on group sequential test without SSR (general case).
#'
#' @noRd
#'
.getFinalConfidenceIntervalMeansGroupSequential <- function(..., design, dataInput, stage,
thetaH0 = C_THETA_H0_MEANS_DEFAULT, directionUpper = C_DIRECTION_UPPER_DEFAULT,
normalApproximation = C_NORMAL_APPROXIMATION_MEANS_DEFAULT,
equalVariances = C_EQUAL_VARIANCES_DEFAULT, tolerance = C_ANALYSIS_TOLERANCE_DEFAULT) {
stageResults <- .getStageResultsMeans(
design = design, dataInput = dataInput, stage = stage,
thetaH0 = thetaH0, directionUpper = directionUpper, normalApproximation = normalApproximation,
equalVariances = equalVariances
)
finalConfidenceIntervalMeansValues <- .getFinalConfidenceIntervalMeansValues(
design, dataInput, stageResults, directionUpper, thetaH0, stage, tolerance
)
return(list(
stage = stage,
thetaH0 = thetaH0,
directionUpper = directionUpper,
normalApproximation = normalApproximation,
equalVariances = equalVariances,
tolerance = tolerance,
finalStage = finalConfidenceIntervalMeansValues$finalStage,
medianUnbiasedGeneral = finalConfidenceIntervalMeansValues$medianUnbiasedGeneral,
finalConfidenceIntervalGeneral = finalConfidenceIntervalMeansValues$finalConfidenceIntervalGeneral,
medianUnbiased = finalConfidenceIntervalMeansValues$medianUnbiased,
finalConfidenceInterval = finalConfidenceIntervalMeansValues$finalConfidenceInterval
))
}
.getFinalConfidenceIntervalMeansValues <- function(design, dataInput,
stageResults, directionUpper, thetaH0, stage, tolerance) {
finalConfidenceIntervalGeneral <- rep(NA_real_, 2)
medianUnbiasedGeneral <- NA_real_
if (.isTrialDesignGroupSequential(design)) {
designStage <- .getStageGroupSeq(design = design, stageResults = stageResults, stage = stage)
} else {
designStage <- .getStageInverseNormal(design = design, stageResults = stageResults, stage = stage)
}
finalStage <- min(designStage, design$kMax)
# early stopping or at end of study
if (designStage < design$kMax || stage == design$kMax) {
if (designStage == 1) {
if (.isTrialDesignGroupSequential(design)) {
medianUnbiasedGeneral <- .getOneMinusQNorm(stageResults$overallPValues[1])
} else {
medianUnbiasedGeneral <- stageResults$combInverseNormal[1]
}
finalConfidenceIntervalGeneral[1] <- medianUnbiasedGeneral -
.getOneMinusQNorm(design$alpha / design$sided)
finalConfidenceIntervalGeneral[2] <- medianUnbiasedGeneral +
.getOneMinusQNorm(design$alpha / design$sided)
if (dataInput$getNumberOfGroups() == 1) {
finalConfidenceIntervalGeneral <- finalConfidenceIntervalGeneral /
sqrt(stageResults$overallSampleSizes[1])
medianUnbiasedGeneral <- medianUnbiasedGeneral /
sqrt(stageResults$overallSampleSizes[1])
} else {
finalConfidenceIntervalGeneral <- finalConfidenceIntervalGeneral *
sqrt(1 / stageResults$overallSampleSizes1[finalStage] +
1 / stageResults$overallSampleSizes2[finalStage])
medianUnbiasedGeneral <- medianUnbiasedGeneral *
sqrt(1 / stageResults$overallSampleSizes1[finalStage] +
1 / stageResults$overallSampleSizes2[finalStage])
}
} else {
if (.isTrialDesignInverseNormal(design) && design$kMax > 2 && !.isNoEarlyEfficacy(design)) {
message(
"Calculation of final confidence interval performed for kMax = ", design$kMax,
" (for kMax > 2, it is theoretically shown that it is valid only ",
"if no sample size change was performed)"
)
}
firstParameterName <- ifelse(.isTrialDesignGroupSequential(design),
"overallPValues", "combInverseNormal"
)
finalConfidenceIntervalGeneral[1] <- .getDecisionMatrixRoot(
design = design,
stage = finalStage, stageResults = stageResults, tolerance = tolerance,
firstParameterName = firstParameterName,
case = "finalConfidenceIntervalGeneralLower"
)
finalConfidenceIntervalGeneral[2] <- .getDecisionMatrixRoot(
design = design,
stage = finalStage, stageResults = stageResults, tolerance = tolerance,
firstParameterName = firstParameterName,
case = "finalConfidenceIntervalGeneralUpper"
)
medianUnbiasedGeneral <- .getDecisionMatrixRoot(
design = design,
stage = finalStage, stageResults = stageResults, tolerance = tolerance,
firstParameterName = firstParameterName,
case = "medianUnbiasedGeneral"
)
}
}
if (designStage > 1 && is.na(finalConfidenceIntervalGeneral[1])) {
finalStage <- NA_integer_
}
finalConfidenceInterval <- rep(NA_real_, 2)
medianUnbiased <- NA_real_
if (!is.na(finalStage)) {
if (designStage == 1) {
# retransformation
if (dataInput$getNumberOfGroups() == 1) {
stdErr <- stageResults$overallStDevs[finalStage] /
sqrt(stageResults$overallSampleSizes[finalStage])
} else {
stdErr <- stageResults$overallStDevs[finalStage] *
sqrt(1 / stageResults$overallSampleSizes1[finalStage] +
1 / stageResults$overallSampleSizes2[finalStage])
}
value <- .getOneMinusQNorm(design$alpha / design$sided) * stdErr
medianUnbiased <- stageResults$effectSizes[1]
finalConfidenceInterval[1] <- medianUnbiased - value
finalConfidenceInterval[2] <- medianUnbiased + value
} else {
directionUpperSign <- ifelse(directionUpper, 1, -1)
finalConfidenceInterval <- finalConfidenceIntervalGeneral *
stageResults$overallStDevs[finalStage] + directionUpperSign * thetaH0
medianUnbiased <- medianUnbiasedGeneral *
stageResults$overallStDevs[finalStage] + directionUpperSign * thetaH0
}
}
if (!directionUpper) {
medianUnbiasedGeneral <- -medianUnbiasedGeneral
finalConfidenceIntervalGeneral <- -finalConfidenceIntervalGeneral
if (designStage > 1) {
medianUnbiased <- -medianUnbiased
finalConfidenceInterval <- -finalConfidenceInterval
}
}
if (!any(is.na(finalConfidenceIntervalGeneral))) {
finalConfidenceIntervalGeneral <- sort(finalConfidenceIntervalGeneral)
}
if (!any(is.na(finalConfidenceInterval))) {
finalConfidenceInterval <- sort(finalConfidenceInterval)
}
return(list(
finalStage = finalStage,
medianUnbiasedGeneral = medianUnbiasedGeneral,
finalConfidenceIntervalGeneral = finalConfidenceIntervalGeneral,
medianUnbiased = medianUnbiased,
finalConfidenceInterval = finalConfidenceInterval
))
}
#'
#' Calculation of final confidence interval
#' based on inverse normal method, only theoretically shown to be valid for kMax <= 2 or no SSR.
#'
#' @noRd
#'
.getFinalConfidenceIntervalMeansInverseNormal <- function(..., design, dataInput, stage,
thetaH0 = C_THETA_H0_MEANS_DEFAULT, directionUpper = C_DIRECTION_UPPER_DEFAULT,
normalApproximation = C_NORMAL_APPROXIMATION_MEANS_DEFAULT, equalVariances = C_EQUAL_VARIANCES_DEFAULT,
tolerance = C_ANALYSIS_TOLERANCE_DEFAULT) {
stageResults <- .getStageResultsMeans(
design = design, dataInput = dataInput, stage = stage,
thetaH0 = thetaH0, directionUpper = directionUpper, normalApproximation = normalApproximation,
equalVariances = equalVariances
)
finalConfidenceIntervalMeansValues <- .getFinalConfidenceIntervalMeansValues(
design, dataInput, stageResults, directionUpper, thetaH0, stage, tolerance
)
return(list(
stage = stage,
thetaH0 = thetaH0,
directionUpper = directionUpper,
normalApproximation = normalApproximation,
equalVariances = equalVariances,
tolerance = tolerance,
finalStage = finalConfidenceIntervalMeansValues$finalStage,
medianUnbiasedGeneral = finalConfidenceIntervalMeansValues$medianUnbiasedGeneral,
finalConfidenceIntervalGeneral = finalConfidenceIntervalMeansValues$finalConfidenceIntervalGeneral,
medianUnbiased = finalConfidenceIntervalMeansValues$medianUnbiased,
finalConfidenceInterval = finalConfidenceIntervalMeansValues$finalConfidenceInterval
))
}
.getQFunctionResultBasedOnDataInput <- function(..., design, dataInput, theta, stage, infRate,
directionUpper, normalApproximation, equalVariances) {
if (dataInput$getNumberOfGroups() == 1) {
stageResults <- .getStageResultsMeans(
design = design, dataInput = dataInput, stage = stage,
thetaH0 = theta, directionUpper = directionUpper, normalApproximation = normalApproximation
)
}
if (dataInput$getNumberOfGroups() == 2) {
stageResults <- .getStageResultsMeans(
design = design, dataInput = dataInput, stage = stage,
thetaH0 = theta, directionUpper = directionUpper, normalApproximation = normalApproximation,
equalVariances = equalVariances
)
}
return(.getQFunctionResult(
design = design, stageResults = stageResults,
theta = theta, infRate = infRate
))
}
#'
#' Calculation of final confidence interval
#' based on Fisher combination test, only valid for kMax <= 2.
#'
#' @noRd
#'
.getFinalConfidenceIntervalMeansFisher <- function(..., design, dataInput, stage,
thetaH0 = C_THETA_H0_MEANS_DEFAULT, directionUpper = C_DIRECTION_UPPER_DEFAULT,
normalApproximation = C_NORMAL_APPROXIMATION_MEANS_DEFAULT, equalVariances = C_EQUAL_VARIANCES_DEFAULT,
tolerance = C_ANALYSIS_TOLERANCE_DEFAULT) {
stageResults <- .getStageResultsMeans(
design = design, dataInput = dataInput, stage = stage,
thetaH0 = thetaH0, directionUpper = directionUpper, normalApproximation = normalApproximation,
equalVariances = equalVariances
)
stageFisher <- .getStageFisher(design = design, stageResults = stageResults, stage = stage)
finalStage <- min(stageFisher, design$kMax)
finalConfidenceInterval <- rep(NA_real_, 2)
medianUnbiased <- NA_real_
# early stopping or at end of study
if (stageFisher < design$kMax || stage == design$kMax) {
if (dataInput$getNumberOfGroups() == 1) {
infRate <- sqrt(stageResults$overallSampleSizes[1])
stderr <- stageResults$overallStDevs[finalStage] /
sqrt(stageResults$overallSampleSizes[finalStage])
} else {
infRate <- 1 / sqrt(1 / stageResults$overallSampleSizes1[1] +
1 / stageResults$overallSampleSizes2[1])
stderr <- stageResults$overallStDevs[finalStage] *
sqrt(1 / stageResults$overallSampleSizes1[finalStage] +
1 / stageResults$overallSampleSizes2[finalStage])
}
if (stageFisher == 1) {
finalConfidenceInterval[1] <- stageResults$effectSizes[1] -
.getOneMinusQNorm(design$alpha / design$sided) * stderr
finalConfidenceInterval[2] <- stageResults$effectSizes[1] +
.getOneMinusQNorm(design$alpha / design$sided) * stderr
medianUnbiased <- stageResults$effectSizes[1]
} else {
maxSearchIterations <- 50
if (design$kMax >= 1) {
message(
"Calculation of final confidence interval for Fisher's ",
"design not implemented yet"
)
return(list(
finalStage = NA_integer_, medianUnbiased = NA_real_,
finalConfidenceInterval = rep(NA_real_, design$kMax)
))
}
thetaLow <- -1
.getQFunctionResult(
design = design, stageResults = stageResults,
theta = thetaLow, infRate = infRate
)
iteration <- 0
while (iteration <= maxSearchIterations &&
.getQFunctionResultBasedOnDataInput(
design = design, dataInput = dataInput,
theta = thetaLow, stage = finalStage,
infRate = infRate, directionUpper = directionUpper,
normalApproximation = normalApproximation,
equalVariances = equalVariances
) > design$alpha / design$sided) {
thetaLow <- 2 * thetaLow
iteration <- iteration + 1
if (iteration == maxSearchIterations) {
thetaLow <- -1
}
}
thetaUp <- 1
iteration <- 0
while (iteration <= maxSearchIterations &&
.getQFunctionResultBasedOnDataInput(
design = design, dataInput = dataInput,
theta = thetaUp, stage = finalStage,
infRate = infRate, directionUpper = directionUpper,
normalApproximation = normalApproximation,
equalVariances = equalVariances
) < 1 - design$alpha / design$sided) {
thetaUp <- 2 * thetaUp
iteration <- iteration + 1
if (iteration == maxSearchIterations) {
thetaUp <- 1
}
}
finalConfidenceInterval[1] <- .getOneDimensionalRoot(
function(theta) {
return(.getQFunctionResultBasedOnDataInput(
design = design, dataInput = dataInput,
theta = theta, stage = finalStage,
infRate = infRate, directionUpper = directionUpper,
normalApproximation = normalApproximation,
equalVariances = equalVariances
) - design$alpha / design$sided)
},
lower = thetaLow, upper = thetaUp, tolerance = tolerance,
callingFunctionInformation = "Final confidence interval Fisher [1]"
)
finalConfidenceInterval[2] <- .getOneDimensionalRoot(
function(theta) {
return(.getQFunctionResultBasedOnDataInput(
design = design, dataInput = dataInput,
theta = theta, stage = finalStage,
infRate = infRate, directionUpper = directionUpper,
normalApproximation = normalApproximation,
equalVariances = equalVariances
) - 1 + design$alpha / design$sided)
},
lower = thetaLow, upper = thetaUp, tolerance = tolerance,
callingFunctionInformation = "Final confidence interval Fisher [2]"
)
medianUnbiased <- .getOneDimensionalRoot(
function(theta) {
return(.getQFunctionResultBasedOnDataInput(
design = design, dataInput = dataInput,
theta = theta, stage = finalStage,
infRate = infRate, directionUpper = directionUpper,
normalApproximation = normalApproximation, equalVariances = equalVariances
) - 0.5)
},
lower = thetaLow, upper = thetaUp, tolerance = tolerance,
callingFunctionInformation = "Final confidence interval Fisher, median unbiased"
)
}
if (is.na(finalConfidenceInterval[1])) {
finalStage <- NA_integer_
}
}
return(list(
stage = stage,
thetaH0 = thetaH0,
directionUpper = directionUpper,
normalApproximation = normalApproximation,
equalVariances = equalVariances,
tolerance = tolerance,
finalStage = finalStage,
medianUnbiased = medianUnbiased,
finalConfidenceInterval = finalConfidenceInterval
))
}
.getFinalConfidenceIntervalMeans <- function(..., design, dataInput,
thetaH0 = NA_real_, directionUpper = C_DIRECTION_UPPER_DEFAULT,
normalApproximation = C_NORMAL_APPROXIMATION_MEANS_DEFAULT, equalVariances = C_EQUAL_VARIANCES_DEFAULT,
tolerance = C_ANALYSIS_TOLERANCE_DEFAULT) {
stage <- .getStageFromOptionalArguments(..., dataInput = dataInput, design = design)
.assertIsValidThetaH0DataInput(thetaH0, dataInput)
.warnInCaseOfUnknownArguments(
functionName = "getFinalConfidenceIntervalMeans",
ignore = c(.getDesignArgumentsToIgnoreAtUnknownArgumentCheck(design, powerCalculationEnabled = TRUE), "stage"), ...
)
if (design$kMax == 1) {
return(list(
finalStage = NA_integer_,
medianUnbiasedGeneral = NA_real_,
finalConfidenceIntervalGeneral = c(NA_real_, NA_real_),
medianUnbiased = NA_real_,
finalConfidenceInterval = c(NA_real_)
))
}
if (is.na(thetaH0)) {
thetaH0 <- C_THETA_H0_MEANS_DEFAULT
}
if (.isTrialDesignGroupSequential(design)) {
return(.getFinalConfidenceIntervalMeansGroupSequential(
design = design, dataInput = dataInput, stage = stage, thetaH0 = thetaH0,
directionUpper = directionUpper, normalApproximation = normalApproximation,
equalVariances = equalVariances, tolerance = tolerance
))
}
if (.isTrialDesignInverseNormal(design)) {
return(.getFinalConfidenceIntervalMeansInverseNormal(
design = design, dataInput = dataInput, stage = stage, thetaH0 = thetaH0,
directionUpper = directionUpper, normalApproximation = normalApproximation,
equalVariances = equalVariances, tolerance = tolerance
))
}
if (.isTrialDesignFisher(design)) {
return(.getFinalConfidenceIntervalMeansFisher(
design = design, dataInput = dataInput, stage = stage, thetaH0 = thetaH0,
directionUpper = directionUpper, normalApproximation = normalApproximation,
equalVariances = equalVariances, tolerance = tolerance
))
}
.stopWithWrongDesignMessage(design, inclusiveConditionalDunnett = FALSE)
}
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