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Merge pull request #56 from rpact-com/dev/4.0.1
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Release candidate RC2
fpahlke authored Sep 24, 2024

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2 parents 2b03b90 + bc562f7 commit dbc7461
Showing 30 changed files with 234 additions and 201 deletions.
4 changes: 2 additions & 2 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: rpact
Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Version: 4.0.1.9261
Date: 2024-09-20
Version: 4.0.1.9262
Date: 2024-09-23
Authors@R: c(
person(
given = "Gernot",
103 changes: 40 additions & 63 deletions R/class_summary.R
Original file line number Diff line number Diff line change
@@ -13,8 +13,8 @@
## |
## | Contact us for information about our services: [email protected]
## |
## | File version: $Revision: 8246 $
## | Last changed: $Date: 2024-09-20 12:10:36 +0200 (Fr, 20 Sep 2024) $
## | File version: $Revision: 8252 $
## | Last changed: $Date: 2024-09-23 13:03:24 +0200 (Mo, 23 Sep 2024) $
## | Last changed by: $Author: pahlke $
## |

@@ -1035,7 +1035,7 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
}
} else if (!is.null(parameterName) && length(parameterName) == 1 && !is.na(parameterName)) {
if (parameterName == "futilityBounds") {
values[!is.na(values) & values <= -6] <- -Inf
values[!is.na(values) & values <= C_FUTILITY_BOUNDS_DEFAULT] <- -Inf
} else if (parameterName %in% c(
"criticalValues",
"decisionCriticalValue", "overallAdjustedTestStatistics"
@@ -1899,7 +1899,7 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
}
if (!.isDelayedInformationEnabled(design = design) &&
((.isTrialDesignInverseNormalOrGroupSequential(design) &&
any(design$futilityBounds > -6, na.rm = TRUE)) ||
any(design$futilityBounds > C_FUTILITY_BOUNDS_DEFAULT, na.rm = TRUE)) ||
(.isTrialDesignFisher(design) && any(design$alpha0Vec < 1)))) {
header <- .concatenateSummaryText(
header,
@@ -3194,7 +3194,7 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
)
}
} else {
if (any(design$futilityBounds > -6)) {
if (any(design$futilityBounds > C_FUTILITY_BOUNDS_DEFAULT)) {
summaryFactory$addParameter(design,
parameterName = "futilityBounds",
parameterCaption = .getSummaryParameterCaptionFutilityBounds(design),
@@ -3462,18 +3462,6 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
)
}

if (simulationEnabled && (multiArmEnabled || enrichmentEnabled || countDataEnabled)) {
if (!planningEnabled && !baseEnabled && any(designPlan$futilityPerStage != 0)) {
summaryFactory$addParameter(designPlan,
parameterName = "futilityPerStage",
parameterCaption = "Exit probability for futility", # (under H1)
roundDigits = digitSettings$digitsProbabilities,
smoothedZeroFormat = TRUE,
transpose = TRUE
)
}
}

if (baseEnabled) {
parameterName <- "rejectPerStage"
if (design$kMax == 1) {
@@ -3556,15 +3544,6 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
}

if (simulationEnabled && (multiArmEnabled || enrichmentEnabled || countDataEnabled)) {
if (!planningEnabled && !baseEnabled && any(designPlan$futilityPerStage != 0)) {
summaryFactory$addParameter(designPlan,
parameterName = "futilityPerStage",
parameterCaption = "Exit probability for futility", # (under H1)
roundDigits = digitSettings$digitsProbabilities,
smoothedZeroFormat = TRUE,
transpose = TRUE
)
}

if (survivalEnabled) {
summaryFactory$addParameter(designPlan,
@@ -3820,17 +3799,6 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
)
}

if (baseEnabled && !planningEnabled && !is.null(designPlan[["futilityPerStage"]]) &&
!any(is.na(designPlan[["futilityPerStage"]])) &&
any(designPlan$futilityPerStage != 0) && any(designPlan$futilityPerStage > 1e-08)) {
summaryFactory$addParameter(designPlan,
parameterName = "futilityPerStage",
parameterCaption = "Exit probability for futility", # (under H1)
roundDigits = digitSettings$digitsProbabilities,
smoothedZeroFormat = TRUE
)
}

probsH0 <- NULL
probsH1 <- NULL
if (design$kMax > 1) {
@@ -3862,24 +3830,6 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
}
}

if (baseEnabled && simulationEnabled && design$kMax > 1) {
values <- NULL
if (!is.null(probsH1)) {
if (is.matrix(probsH1$rejectPerStage)) {
values <- matrix(probsH1$rejectPerStage[1:(design$kMax - 1), ], ncol = ncol(probsH1$rejectPerStage))
} else {
values <- probsH1$rejectPerStage[1:(design$kMax - 1)]
}
}
summaryFactory$addParameter(designPlan,
parameterName = "rejectPerStage",
values = values,
parameterCaption = "Exit probability for efficacy",
roundDigits = digitSettings$digitsProbabilities,
smoothedZeroFormat = TRUE
)
}

if (planningEnabled) {
if (!is.null(probsH1) && !is.null(probsH0) && design$kMax > 1) {
probsH0$earlyStop <- matrix(probsH0$earlyStop[1:(design$kMax - 1), 1], ncol = 1)
@@ -3897,7 +3847,7 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
probsH1$rejectPerStage <- probsH1$rejectPerStage[1:(design$kMax - 1)]
}

if (any(design$futilityBounds > -6)) {
if (any(design$futilityBounds > C_FUTILITY_BOUNDS_DEFAULT)) {
if (is.matrix(probsH1$earlyStop)) {
probsH1$earlyStop <- matrix(probsH1$earlyStop[1:(design$kMax - 1), ],
ncol = ncol(probsH1$earlyStop)
@@ -3946,22 +3896,18 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
)
}

if (any(design$futilityBounds > -6)) {
if (any(design$futilityBounds > C_FUTILITY_BOUNDS_DEFAULT, na.rm = TRUE)) {
summaryFactory$addParameter(probsH0,
parameterName = "futilityPerStage",
parameterCaption = "Exit probability for futility (under H0)",
roundDigits = digitSettings$digitsProbabilities,
smoothedZeroFormat = TRUE
)
x <- designPlan
if (is.null(x)) {
x <- design
}
futilityPerStage <- probsH1$futilityPerStage
if (.isTrialDesignPlan(x) && x$.isSampleSizeObject() && ncol(futilityPerStage) > 1) {
if (designPlan$.isSampleSizeObject() && ncol(futilityPerStage) > 1) {
futilityPerStage <- futilityPerStage[, 1]
}
summaryFactory$addParameter(x,
summaryFactory$addParameter(designPlan,
parameterName = "futilityPerStage",
values = futilityPerStage,
parameterCaption = "Exit probability for futility (under H1)",
@@ -3970,6 +3916,37 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
)
}
}
} else {
rejectPerStageValues <- NULL
if (!is.null(probsH1)) {
if (is.matrix(probsH1$rejectPerStage)) {
rejectPerStageValues <- matrix(probsH1$rejectPerStage[1:(design$kMax - 1), ], ncol = ncol(probsH1$rejectPerStage))
} else {
rejectPerStageValues <- probsH1$rejectPerStage[1:(design$kMax - 1)]
}
}
if (!is.null(rejectPerStageValues)) {
summaryFactory$addParameter(designPlan,
parameterName = "rejectPerStage",
values = rejectPerStageValues,
parameterCaption = "Exit probability for efficacy",
roundDigits = digitSettings$digitsProbabilities,
smoothedZeroFormat = TRUE
)
}

if (any(design$futilityBounds > C_FUTILITY_BOUNDS_DEFAULT, na.rm = TRUE) &&
!is.null(designPlan[["futilityPerStage"]]) &&
!any(is.na(designPlan[["futilityPerStage"]])) &&
any(designPlan$futilityPerStage != 0) && any(designPlan$futilityPerStage > 1e-08)) {
summaryFactory$addParameter(designPlan,
parameterName = "futilityPerStage",
parameterCaption = "Exit probability for futility", # under H1
roundDigits = digitSettings$digitsProbabilities,
smoothedZeroFormat = TRUE,
transpose = grepl("MultiArm|Enrichment", .getClassName(designPlan))
)
}
}

if (!is.null(performanceScore)) {
168 changes: 112 additions & 56 deletions R/f_design_plan_means.R
Original file line number Diff line number Diff line change
@@ -13,8 +13,8 @@
## |
## | Contact us for information about our services: info@rpact.com
## |
## | File version: $Revision: 8247 $
## | Last changed: $Date: 2024-09-20 12:27:05 +0200 (Fr, 20 Sep 2024) $
## | File version: $Revision: 8252 $
## | Last changed: $Date: 2024-09-23 13:03:24 +0200 (Mo, 23 Sep 2024) $
## | Last changed by: $Author: pahlke $
## |

@@ -39,28 +39,41 @@ NULL
} else {
criticalValues <- stats::qt(
1 - design$stageLevels,
design$informationRates %*% t(maxNumberOfSubjects) - designPlan$groups
pmax(design$informationRates %*% t(maxNumberOfSubjects) - designPlan$groups, 1E-4)
)

# outside validated range
numberOfNAs <- sum(as.vector(criticalValues) > 50, na.rm = TRUE)
criticalValues[criticalValues > 50] <- NA_real_

if (any(is.na(criticalValues))) {
warning("The computation of ", .integerToWrittenNumber(numberOfNAs),
" efficacy boundar", ifelse(numberOfNAs == 1, "y", "ies"), " on ",
"treatment effect scale not performed presumably due to too small df",
warning("The computation of ", .integerToWrittenNumber(numberOfNAs), " ",
"efficacy boundar", ifelse(numberOfNAs == 1, "y", "ies"), " ",
"on treatment effect scale not performed presumably ",
"due to too small degrees of freedom",
call. = FALSE
)
}

futilityBounds <- stats::qt(
stats::pnorm(design$futilityBounds),
design$informationRates[1:(design$kMax - 1)] %*% t(maxNumberOfSubjects) - designPlan$groups
)
if (any(design$futilityBounds > C_FUTILITY_BOUNDS_DEFAULT, na.rm = TRUE)) {
futilityBounds <- stats::qt(
stats::pnorm(design$futilityBounds),
pmax(design$informationRates[1:(design$kMax - 1)] %*%
t(maxNumberOfSubjects) - designPlan$groups, 1e-04)
)

# outside validated range
futilityBounds[futilityBounds < -50] <- NA_real_
# outside validated range
futilityBounds[abs(futilityBounds) > 50] <- NA_real_
if (any(is.na(futilityBounds))) {
warning("The computation of futility boundar",
ifelse(numberOfNAs == 1, "y", "ies"), " ",
"on treatment effect scale not performed presumably ",
"due to too small degrees of freedom",
call. = FALSE
)
}
} else {
futilityBounds <- design$futilityBounds
}
}
futilityBounds[!is.na(futilityBounds) & futilityBounds <= C_FUTILITY_BOUNDS_DEFAULT] <- NA_real_

@@ -74,7 +87,8 @@ NULL
sqrt(design$informationRates[1:(design$kMax - 1)] %*% t(maxNumberOfSubjects))
}
if (!.isTrialDesignFisher(design) && design$sided == 2 && design$kMax > 1 &&
(design$typeOfDesign == C_TYPE_OF_DESIGN_PT || !is.null(design$typeBetaSpending) && design$typeBetaSpending != "none")) {
(design$typeOfDesign == C_TYPE_OF_DESIGN_PT ||
!is.null(design$typeBetaSpending) && design$typeBetaSpending != "none")) {
futilityBoundsEffectScaleLower <- thetaH0 - futilityBounds * stDev /
sqrt(design$informationRates[1:(design$kMax - 1)] %*% t(maxNumberOfSubjects))
}
@@ -91,7 +105,8 @@ NULL
design$informationRates[1:(design$kMax - 1)] %*% t(maxNumberOfSubjects)))
}
if (!.isTrialDesignFisher(design) && design$sided == 2 && design$kMax > 1 &&
(design$typeOfDesign == C_TYPE_OF_DESIGN_PT || !is.null(design$typeBetaSpending) && design$typeBetaSpending != "none")) {
(design$typeOfDesign == C_TYPE_OF_DESIGN_PT ||
!is.null(design$typeBetaSpending) && design$typeBetaSpending != "none")) {
futilityBoundsEffectScaleLower <- thetaH0 - futilityBounds * stDev *
(1 + allocationRatioPlanned) / (sqrt(allocationRatioPlanned *
design$informationRates[1:(design$kMax - 1)] %*% t(maxNumberOfSubjects)))
@@ -111,7 +126,8 @@ NULL
(sqrt(design$informationRates[1:(design$kMax - 1)] %*% t(maxNumberOfSubjects)))
}
if (!.isTrialDesignFisher(design) && design$sided == 2 && design$kMax > 1 &&
(design$typeOfDesign == C_TYPE_OF_DESIGN_PT || !is.null(design$typeBetaSpending) && design$typeBetaSpending != "none")) {
(design$typeOfDesign == C_TYPE_OF_DESIGN_PT ||
!is.null(design$typeBetaSpending) && design$typeBetaSpending != "none")) {
futilityBoundsEffectScaleLower <- thetaH0 - futilityBounds * stDev *
sqrt(1 + 1 / allocationRatioPlanned + thetaH0^2 * (1 + allocationRatioPlanned)) /
(sqrt(design$informationRates[1:(design$kMax - 1)] %*% t(maxNumberOfSubjects)))
@@ -128,17 +144,33 @@ NULL
}
}
if (designPlan$meanRatio) {
criticalValuesEffectScaleUpper[!is.na(criticalValuesEffectScaleUpper) & criticalValuesEffectScaleUpper <= 0] <- NA_real_
criticalValuesEffectScaleLower[!is.na(criticalValuesEffectScaleLower) & criticalValuesEffectScaleLower <= 0] <- NA_real_
futilityBoundsEffectScaleUpper[!is.na(futilityBoundsEffectScaleUpper) & futilityBoundsEffectScaleUpper <= 0] <- NA_real_
futilityBoundsEffectScaleLower[!is.na(futilityBoundsEffectScaleLower) & futilityBoundsEffectScaleLower <= 0] <- NA_real_
criticalValuesEffectScaleUpper[!is.na(criticalValuesEffectScaleUpper) &
criticalValuesEffectScaleUpper <= 0] <- NA_real_
criticalValuesEffectScaleLower[!is.na(criticalValuesEffectScaleLower) &
criticalValuesEffectScaleLower <= 0] <- NA_real_
futilityBoundsEffectScaleUpper[!is.na(futilityBoundsEffectScaleUpper) &
futilityBoundsEffectScaleUpper <= 0] <- NA_real_
futilityBoundsEffectScaleLower[!is.na(futilityBoundsEffectScaleLower) &
futilityBoundsEffectScaleLower <= 0] <- NA_real_
}

return(list(
criticalValuesEffectScaleUpper = matrix(criticalValuesEffectScaleUpper, nrow = design$kMax),
criticalValuesEffectScaleLower = matrix(criticalValuesEffectScaleLower, nrow = design$kMax),
futilityBoundsEffectScaleUpper = matrix(futilityBoundsEffectScaleUpper, nrow = design$kMax - 1),
futilityBoundsEffectScaleLower = matrix(futilityBoundsEffectScaleLower, nrow = design$kMax - 1)
criticalValuesEffectScaleUpper = matrix(
criticalValuesEffectScaleUpper,
nrow = design$kMax
),
criticalValuesEffectScaleLower = matrix(
criticalValuesEffectScaleLower,
nrow = design$kMax
),
futilityBoundsEffectScaleUpper = matrix(
futilityBoundsEffectScaleUpper,
nrow = design$kMax - 1
),
futilityBoundsEffectScaleLower = matrix(
futilityBoundsEffectScaleLower,
nrow = design$kMax - 1
)
))
}

@@ -207,7 +239,8 @@ NULL
} else {
nFixed[i] <- .getOneDimensionalRoot(
function(n) {
return(stats::pnorm(.getOneMinusQNorm(alpha / 2) - sqrt(n) * (theta - thetaH0) / stDev) -
return(stats::pnorm(.getOneMinusQNorm(alpha / 2) -
sqrt(n) * (theta - thetaH0) / stDev) -
stats::pnorm(-.getOneMinusQNorm(alpha / 2) - sqrt(n) * (theta - thetaH0) / stDev) - beta)
},
lower = 0.001, upper = up, tolerance = 1e-04,
@@ -482,16 +515,16 @@ NULL

# Note that 'directionUpper' and 'maxNumberOfSubjects' are only applicable
# for 'objectType' = "power"
.createDesignPlanMeans <- function(...,
.createDesignPlanMeans <- function(...,
objectType = c("sampleSize", "power"),
design,
normalApproximation = FALSE,
design,
normalApproximation = FALSE,
meanRatio = FALSE,
thetaH0 = ifelse(meanRatio, 1, 0),
thetaH0 = ifelse(meanRatio, 1, 0),
alternative = NA_real_,
stDev = C_STDEV_DEFAULT,
stDev = C_STDEV_DEFAULT,
directionUpper = NA,
maxNumberOfSubjects = NA_real_,
maxNumberOfSubjects = NA_real_,
groups = 2,
allocationRatioPlanned = NA_real_) {
objectType <- match.arg(objectType)
@@ -505,16 +538,18 @@ NULL
.assertIsSingleLogical(meanRatio, "meanRatio")
.assertIsValidThetaH0(thetaH0, endpoint = "means", groups = groups, ratioEnabled = meanRatio)
.assertIsSingleLogical(normalApproximation, "normalApproximation")

if (meanRatio) {
if (identical(alternative, C_ALTERNATIVE_POWER_SIMULATION_DEFAULT)) {
alternative <- C_ALTERNATIVE_POWER_SIMULATION_MEAN_RATIO_DEFAULT
}
.assertIsInOpenInterval(alternative, "alternative", 0, NULL, naAllowed = TRUE)
}

directionUpper <- .assertIsValidDirectionUpper(directionUpper,
design, objectType = objectType, userFunctionCallEnabled = TRUE)
directionUpper <- .assertIsValidDirectionUpper(directionUpper,
design,
objectType = objectType, userFunctionCallEnabled = TRUE
)

if (objectType == "sampleSize" && !any(is.na(alternative))) {
if (design$sided == 1 && any(alternative - thetaH0 <= 0)) {
@@ -549,10 +584,12 @@ NULL
}

if (groups == 2) {
if (design$sided == 2 && ((thetaH0 != 0 && !meanRatio) || (thetaH0 != 1 && meanRatio))) {
if (design$sided == 2 && ((thetaH0 != 0 && !meanRatio) ||
(thetaH0 != 1 && meanRatio))) {
stop(
C_EXCEPTION_TYPE_ILLEGAL_ARGUMENT,
"two-sided case is implemented only for superiority testing (i.e., thetaH0 = ", ifelse(meanRatio, 1, 0), ")"
"two-sided case is implemented only for superiority testing ",
"(i.e., thetaH0 = ", ifelse(meanRatio, 1, 0), ")"
)
}

@@ -581,7 +618,10 @@ NULL
}
}

.setValueAndParameterType(designPlan, "normalApproximation", normalApproximation, FALSE)
.setValueAndParameterType(
designPlan, "normalApproximation",
normalApproximation, FALSE
)
.setValueAndParameterType(designPlan, "meanRatio", meanRatio, FALSE)
.setValueAndParameterType(designPlan, "thetaH0", thetaH0, 0)
if (objectType == "power") {
@@ -590,12 +630,18 @@ NULL
C_ALTERNATIVE_POWER_SIMULATION_DEFAULT
)
} else {
.setValueAndParameterType(designPlan, "alternative", alternative, C_ALTERNATIVE_DEFAULT)
.setValueAndParameterType(
designPlan, "alternative",
alternative, C_ALTERNATIVE_DEFAULT
)
}
.setValueAndParameterType(designPlan, "stDev", stDev, C_STDEV_DEFAULT)
if (objectType == "power") {
.assertIsValidMaxNumberOfSubjects(maxNumberOfSubjects)
.setValueAndParameterType(designPlan, "maxNumberOfSubjects", maxNumberOfSubjects, NA_real_)
.setValueAndParameterType(
designPlan, "maxNumberOfSubjects",
maxNumberOfSubjects, NA_real_
)
.setValueAndParameterType(designPlan, "directionUpper", directionUpper, TRUE)

designPlan$.setParameterType("effect", C_PARAM_GENERATED)
@@ -672,7 +718,10 @@ getSampleSizeMeans <- function(design = NULL, ...,
design <- .getDefaultDesign(..., type = "sampleSize")
.warnInCaseOfUnknownArguments(
functionName = "getSampleSizeMeans",
ignore = .getDesignArgumentsToIgnoreAtUnknownArgumentCheck(design, powerCalculationEnabled = FALSE), ...
ignore = .getDesignArgumentsToIgnoreAtUnknownArgumentCheck(
design,
powerCalculationEnabled = FALSE
), ...
)
} else {
.assertIsTrialDesign(design)
@@ -683,14 +732,14 @@ getSampleSizeMeans <- function(design = NULL, ...,

designPlan <- .createDesignPlanMeans(
objectType = "sampleSize",
design = design,
normalApproximation = normalApproximation,
design = design,
normalApproximation = normalApproximation,
meanRatio = meanRatio,
thetaH0 = thetaH0,
alternative = alternative,
stDev = stDev,
thetaH0 = thetaH0,
alternative = alternative,
stDev = stDev,
groups = groups,
allocationRatioPlanned = allocationRatioPlanned,
allocationRatioPlanned = allocationRatioPlanned,
...
)

@@ -757,7 +806,10 @@ getPowerMeans <- function(design = NULL, ...,
design <- .getDefaultDesign(..., type = "power")
.warnInCaseOfUnknownArguments(
functionName = "getPowerMeans",
ignore = .getDesignArgumentsToIgnoreAtUnknownArgumentCheck(design, powerCalculationEnabled = TRUE), ...
ignore = .getDesignArgumentsToIgnoreAtUnknownArgumentCheck(
design,
powerCalculationEnabled = TRUE
), ...
)
} else {
.warnInCaseOfUnknownArguments(functionName = "getPowerMeans", ...)
@@ -769,16 +821,16 @@ getPowerMeans <- function(design = NULL, ...,

designPlan <- .createDesignPlanMeans(
objectType = "power",
design = design,
normalApproximation = normalApproximation,
design = design,
normalApproximation = normalApproximation,
meanRatio = meanRatio,
thetaH0 = thetaH0,
alternative = alternative,
stDev = stDev,
thetaH0 = thetaH0,
alternative = alternative,
stDev = stDev,
directionUpper = directionUpper,
maxNumberOfSubjects = maxNumberOfSubjects,
maxNumberOfSubjects = maxNumberOfSubjects,
groups = groups,
allocationRatioPlanned = allocationRatioPlanned,
allocationRatioPlanned = allocationRatioPlanned,
...
)

@@ -804,7 +856,8 @@ getPowerMeans <- function(design = NULL, ...,
}
} else {
if (!designPlan$meanRatio) {
theta <- sqrt(designPlan$allocationRatioPlanned) / (1 + designPlan$allocationRatioPlanned) *
theta <- sqrt(designPlan$allocationRatioPlanned) /
(1 + designPlan$allocationRatioPlanned) *
(designPlan$alternative - designPlan$thetaH0) / designPlan$stDev
} else {
theta <- sqrt(designPlan$allocationRatioPlanned) /
@@ -822,7 +875,10 @@ getPowerMeans <- function(design = NULL, ...,
} else {
thetaAdj <- (sign(theta) * .getOneMinusQNorm(design$alpha / design$sided) -
.getQNorm(stats::pt(
sign(theta) * stats::qt(1 - design$alpha / design$sided, maxNumberOfSubjects - 2),
sign(theta) * stats::qt(
1 - design$alpha / design$sided,
maxNumberOfSubjects - 2
),
maxNumberOfSubjects - 2,
theta * sqrt(maxNumberOfSubjects)
))) / sqrt(maxNumberOfSubjects)
6 changes: 3 additions & 3 deletions tests/testthat/test-class_analysis_dataset.R
Original file line number Diff line number Diff line change
@@ -15,9 +15,9 @@
## |
## | File name: test-class_analysis_dataset.R
## | Creation date: 08 November 2023, 15:29:21
## | File version: $Revision$
## | Last changed: $Date$
## | Last changed by: $Author$
## | File version: $Revision: 7560 $
## | Last changed: $Date: 2024-01-15 14:20:32 +0100 (Mo, 15 Jan 2024) $
## | Last changed by: $Author: pahlke $
## |

test_plan_section("Testing the Class 'Dataset'")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_analysis_base_means.R
Original file line number Diff line number Diff line change
@@ -15,9 +15,9 @@
## |
## | File name: test-f_analysis_base_means.R
## | Creation date: 12 September 2024, 12:48:31
## | File version: $Revision$
## | Last changed: $Date$
## | Last changed by: $Author$
## | File version: $Revision: 8200 $
## | Last changed: $Date: 2024-09-12 15:05:38 +0200 (Do, 12 Sep 2024) $
## | Last changed by: $Author: pahlke $
## |

test_plan_section("Testing the Analysis Means Functionality for One Treatment")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_analysis_base_rates.R
Original file line number Diff line number Diff line change
@@ -15,9 +15,9 @@
## |
## | File name: test-f_analysis_base_rates.R
## | Creation date: 12 September 2024, 12:49:04
## | File version: $Revision$
## | Last changed: $Date$
## | Last changed by: $Author$
## | File version: $Revision: 8200 $
## | Last changed: $Date: 2024-09-12 15:05:38 +0200 (Do, 12 Sep 2024) $
## | Last changed by: $Author: pahlke $
## |

test_plan_section("Testing the Analysis Rates Functionality for One Treatment")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_analysis_base_survival.R
Original file line number Diff line number Diff line change
@@ -15,9 +15,9 @@
## |
## | File name: test-f_analysis_base_survival.R
## | Creation date: 08 November 2023, 08:52:36
## | File version: $Revision$
## | Last changed: $Date$
## | Last changed by: $Author$
## | File version: $Revision: 7560 $
## | Last changed: $Date: 2024-01-15 14:20:32 +0100 (Mo, 15 Jan 2024) $
## | Last changed by: $Author: pahlke $
## |

test_plan_section("Testing the Analysis Survival Functionality for the Group Sequential Design")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_analysis_enrichment_means.R
Original file line number Diff line number Diff line change
@@ -15,9 +15,9 @@
## |
## | File name: test-f_analysis_enrichment_means.R
## | Creation date: 12 September 2024, 12:50:03
## | File version: $Revision$
## | Last changed: $Date$
## | Last changed by: $Author$
## | File version: $Revision: 8200 $
## | Last changed: $Date: 2024-09-12 15:05:38 +0200 (Do, 12 Sep 2024) $
## | Last changed by: $Author: pahlke $
## |

test_that("'getAnalysisResults': stratified analysis, select S1 at first IA, gMax = 2, Fisher design", {
6 changes: 3 additions & 3 deletions tests/testthat/test-f_analysis_enrichment_rates.R
Original file line number Diff line number Diff line change
@@ -15,9 +15,9 @@
## |
## | File name: test-f_analysis_enrichment_rates.R
## | Creation date: 12 September 2024, 12:51:07
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## | File version: $Revision: 8200 $
## | Last changed: $Date: 2024-09-12 15:05:38 +0200 (Do, 12 Sep 2024) $
## | Last changed by: $Author: pahlke $
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test_plan_section("Testing Analysis Enrichment Rates Function")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_analysis_enrichment_survival.R
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## | File name: test-f_analysis_enrichment_survival.R
## | Creation date: 12 September 2024, 12:51:31
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## | Last changed by: $Author: pahlke $
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test_plan_section("Testing Analysis Enrichment Survival Function")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_analysis_multiarm_survival.R
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## | File name: test-f_analysis_multiarm_survival.R
## | Creation date: 08 November 2023, 09:08:43
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test_plan_section("Testing the Analysis Survival Functionality for Three or More Treatments")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_as251.R
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## | File name: test-f_as251.R
## | Creation date: 16 January 2024, 07:16:35
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test_plan_section("Testing Dunnett AS 251 Functions")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_core_assertions.R
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## | File name: test-f_core_assertions.R
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test_plan_section("Testing Assertion Functions")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_core_output_formats.R
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## |
## | File name: test-f_core_output_formats.R
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test_plan_section("Testing the Output Format Functions")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_core_utilities.R
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## |
## | File name: test-f_core_utilities.R
## | Creation date: 08 November 2023, 09:09:36
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test_plan_section("Testing Result Object Print Output")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_design_fisher_combination_test.R
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## | File name: test-f_design_fisher_combination_test.R
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test_plan_section("Testing the Fisher Design Functionality")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_design_group_sequential_beta_spending.R
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## | File name: test-f_design_group_sequential_beta_spending.R
## | Creation date: 08 November 2023, 09:09:55
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test_plan_section("Testing the Group Sequential Design Functionality with Beta Spending")
2 changes: 1 addition & 1 deletion tests/testthat/test-f_design_plan_plot.R
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## | File name: test-f_design_plan_means.R
## | Creation date: 21 December 2023, 08:52:45
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6 changes: 3 additions & 3 deletions tests/testthat/test-f_design_utilities.R
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## | File name: test-f_design_utilities.R
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test_plan_section("Testing Design Utility Functions")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_parameter_set_utilities.R
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## | File name: test-f_parameter_set_utilities.R
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test_plan_section("Testing Parameter Set Utility Functions")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_simulation_base_means.R
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## | File name: test-f_simulation_base_means.R
## | Creation date: 16 September 2024, 08:44:44
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test_plan_section("Testing Simulation Means Function")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_simulation_base_rates.R
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## | File name: test-f_simulation_base_rates.R
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test_plan_section("Testing Simulation Rates Function")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_simulation_base_survival.R
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## | File name: test-f_simulation_base_survival.R
## | Creation date: 16 September 2024, 08:44:51
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test_plan_section("Testing Simulation Survival Function")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_simulation_enrichment_means.R
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## | File name: test-f_simulation_enrichment_means.R
## | Creation date: 08 November 2023, 09:11:08
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test_plan_section("Testing Simulation Enrichment Means Function")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_simulation_enrichment_rates.R
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@@ -15,9 +15,9 @@
## |
## | File name: test-f_simulation_enrichment_rates.R
## | Creation date: 16 September 2024, 09:55:30
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## | File version: $Revision: 8214 $
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test_plan_section("Testing Simulation Enrichment Rates Function")
8 changes: 4 additions & 4 deletions tests/testthat/test-f_simulation_enrichment_survival.R
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@@ -15,9 +15,9 @@
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## | File name: test-f_simulation_enrichment_survival.R
## | Creation date: 16 September 2024, 09:45:06
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test_plan_section("Testing Simulation Enrichment Survival Function")
@@ -57,7 +57,7 @@ test_that("'getSimulationEnrichmentSurvival': gMax = 2", {
)

design <- getDesignInverseNormal(
informationRates = c(0.3, 1),
informationRates = c(0.3, 1),
typeOfDesign = "asUser", userAlphaSpending = c(0.01, 0.025)
)

6 changes: 3 additions & 3 deletions tests/testthat/test-f_simulation_multiarm_means.R
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## | File name: test-f_simulation_multiarm_means.R
## | Creation date: 09 February 2024, 10:57:28
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## | File version: $Revision: 7910 $
## | Last changed: $Date: 2024-05-22 10:02:23 +0200 (Mi, 22 Mai 2024) $
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test_plan_section("Testing Simulation Multi-Arm Means Function")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_simulation_multiarm_rates.R
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## |
## | File name: test-f_simulation_multiarm_rates.R
## | Creation date: 16 September 2024, 09:45:13
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## | File version: $Revision: 8214 $
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test_plan_section("Testing Simulation Multi-Arm Rates Function")
6 changes: 3 additions & 3 deletions tests/testthat/test-f_simulation_multiarm_survival.R
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## | File name: test-f_simulation_multiarm_survival.R
## | Creation date: 12 September 2024, 12:52:12
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## | File version: $Revision: 8200 $
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test_plan_section("Testing Simulation Multi-Arm Survival Function")
6 changes: 3 additions & 3 deletions tests/testthat/test-generic_functions.R
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## | File name: test-generic_functions.R
## | Creation date: 08 November 2023, 09:12:05
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## | File version: $Revision: 7560 $
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test_plan_section("Testing Class 'SummaryFactory'")

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