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Release candidate RC2
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@fpahlke
fpahlke committed Sep 23, 2024
1 parent fe313a7 commit bc562f7
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4 changes: 2 additions & 2 deletions DESCRIPTION
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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",
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103 changes: 40 additions & 63 deletions R/class_summary.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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 $
## |

Expand Down Expand Up @@ -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"
Expand Down Expand Up @@ -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$alpha0Vec < 1)))) {
header <- .concatenateSummaryText(
header,
Expand Down Expand Up @@ -3194,7 +3194,7 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
)
}
} else {
if (any(design$futilityBounds > -6)) {
if (any(design$futilityBounds > C_FUTILITY_BOUNDS_DEFAULT)) {
summaryFactory$addParameter(design,
parameterName = "futilityBounds",
parameterCaption = .getSummaryParameterCaptionFutilityBounds(design),
Expand Down Expand Up @@ -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) {
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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) {
Expand Down Expand Up @@ -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)
Expand All @@ -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)
Expand Down Expand Up @@ -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$addParameter(designPlan,
parameterName = "futilityPerStage",
values = futilityPerStage,
parameterCaption = "Exit probability for futility (under H1)",
Expand All @@ -3970,6 +3916,37 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
)
}
}
} else {
rejectPerStageValues <- NULL
if (!is.null(probsH1)) {
if (is.matrix(probsH1$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)) {
Expand Down
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