-
Notifications
You must be signed in to change notification settings - Fork 5
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Loading status checks…
Merge pull request #56 from rpact-com/dev/4.0.1
Release candidate RC2
Showing
30 changed files
with
234 additions
and
201 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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)) { | ||
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters