diff --git a/DESCRIPTION b/DESCRIPTION index 7fd98e94..df5c345c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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", diff --git a/R/class_summary.R b/R/class_summary.R index 6fd7544d..2ea65b09 100644 --- a/R/class_summary.R +++ b/R/class_summary.R @@ -13,8 +13,8 @@ ## | ## | Contact us for information about our services: info@rpact.com ## | -## | 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)) { diff --git a/R/f_design_plan_means.R b/R/f_design_plan_means.R index 9cb7d597..243c4c94 100644 --- a/R/f_design_plan_means.R +++ b/R/f_design_plan_means.R @@ -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) @@ -505,7 +538,7 @@ 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 @@ -513,8 +546,10 @@ NULL .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) diff --git a/tests/testthat/test-class_analysis_dataset.R b/tests/testthat/test-class_analysis_dataset.R index 80ed5dad..d01a5977 100644 --- a/tests/testthat/test-class_analysis_dataset.R +++ b/tests/testthat/test-class_analysis_dataset.R @@ -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'") diff --git a/tests/testthat/test-f_analysis_base_means.R b/tests/testthat/test-f_analysis_base_means.R index 2d786cec..b685dcd4 100644 --- a/tests/testthat/test-f_analysis_base_means.R +++ b/tests/testthat/test-f_analysis_base_means.R @@ -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") diff --git a/tests/testthat/test-f_analysis_base_rates.R b/tests/testthat/test-f_analysis_base_rates.R index 08f4c514..91d6464b 100644 --- a/tests/testthat/test-f_analysis_base_rates.R +++ b/tests/testthat/test-f_analysis_base_rates.R @@ -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") diff --git a/tests/testthat/test-f_analysis_base_survival.R b/tests/testthat/test-f_analysis_base_survival.R index 9a042520..dd335c2a 100644 --- a/tests/testthat/test-f_analysis_base_survival.R +++ b/tests/testthat/test-f_analysis_base_survival.R @@ -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") diff --git a/tests/testthat/test-f_analysis_enrichment_means.R b/tests/testthat/test-f_analysis_enrichment_means.R index 7b477e49..0a88d0af 100644 --- a/tests/testthat/test-f_analysis_enrichment_means.R +++ b/tests/testthat/test-f_analysis_enrichment_means.R @@ -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", { diff --git a/tests/testthat/test-f_analysis_enrichment_rates.R b/tests/testthat/test-f_analysis_enrichment_rates.R index 08347869..58c4fd94 100644 --- a/tests/testthat/test-f_analysis_enrichment_rates.R +++ b/tests/testthat/test-f_analysis_enrichment_rates.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_analysis_enrichment_rates.R ## | Creation date: 12 September 2024, 12:51:07 -## | 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 Analysis Enrichment Rates Function") diff --git a/tests/testthat/test-f_analysis_enrichment_survival.R b/tests/testthat/test-f_analysis_enrichment_survival.R index 2731ab34..82acbb8f 100644 --- a/tests/testthat/test-f_analysis_enrichment_survival.R +++ b/tests/testthat/test-f_analysis_enrichment_survival.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_analysis_enrichment_survival.R ## | Creation date: 12 September 2024, 12:51:31 -## | 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 Analysis Enrichment Survival Function") diff --git a/tests/testthat/test-f_analysis_multiarm_survival.R b/tests/testthat/test-f_analysis_multiarm_survival.R index 11e15ac4..427ccf2b 100644 --- a/tests/testthat/test-f_analysis_multiarm_survival.R +++ b/tests/testthat/test-f_analysis_multiarm_survival.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_analysis_multiarm_survival.R ## | Creation date: 08 November 2023, 09:08:43 -## | File version: $Revision$ -## | Last changed: $Date$ -## | Last changed by: $Author$ +## | File version: $Revision: 7662 $ +## | Last changed: $Date: 2024-02-23 12:42:26 +0100 (Fr, 23 Feb 2024) $ +## | Last changed by: $Author: pahlke $ ## | test_plan_section("Testing the Analysis Survival Functionality for Three or More Treatments") diff --git a/tests/testthat/test-f_as251.R b/tests/testthat/test-f_as251.R index bab9f346..5576d0da 100644 --- a/tests/testthat/test-f_as251.R +++ b/tests/testthat/test-f_as251.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_as251.R ## | Creation date: 16 January 2024, 07:16:35 -## | File version: $Revision$ -## | Last changed: $Date$ -## | Last changed by: $Author$ +## | File version: $Revision: 7662 $ +## | Last changed: $Date: 2024-02-23 12:42:26 +0100 (Fr, 23 Feb 2024) $ +## | Last changed by: $Author: pahlke $ ## | test_plan_section("Testing Dunnett AS 251 Functions") diff --git a/tests/testthat/test-f_core_assertions.R b/tests/testthat/test-f_core_assertions.R index 2ae6a5e1..fc79f70f 100644 --- a/tests/testthat/test-f_core_assertions.R +++ b/tests/testthat/test-f_core_assertions.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_core_assertions.R ## | Creation date: 08 November 2023, 09:09:35 -## | 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 Assertion Functions") diff --git a/tests/testthat/test-f_core_output_formats.R b/tests/testthat/test-f_core_output_formats.R index 2791473a..78431f5e 100644 --- a/tests/testthat/test-f_core_output_formats.R +++ b/tests/testthat/test-f_core_output_formats.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_core_output_formats.R ## | Creation date: 08 November 2023, 09:09:35 -## | File version: $Revision$ -## | Last changed: $Date$ -## | Last changed by: $Author$ +## | File version: $Revision: 7665 $ +## | Last changed: $Date: 2024-02-23 17:33:46 +0100 (Fr, 23 Feb 2024) $ +## | Last changed by: $Author: pahlke $ ## | test_plan_section("Testing the Output Format Functions") diff --git a/tests/testthat/test-f_core_utilities.R b/tests/testthat/test-f_core_utilities.R index cf776cb6..896a4ba2 100644 --- a/tests/testthat/test-f_core_utilities.R +++ b/tests/testthat/test-f_core_utilities.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_core_utilities.R ## | Creation date: 08 November 2023, 09:09:36 -## | 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 Result Object Print Output") diff --git a/tests/testthat/test-f_design_fisher_combination_test.R b/tests/testthat/test-f_design_fisher_combination_test.R index 0725855c..de249a82 100644 --- a/tests/testthat/test-f_design_fisher_combination_test.R +++ b/tests/testthat/test-f_design_fisher_combination_test.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_design_fisher_combination_test.R ## | Creation date: 08 November 2023, 09:09:43 -## | 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 Fisher Design Functionality") diff --git a/tests/testthat/test-f_design_group_sequential_beta_spending.R b/tests/testthat/test-f_design_group_sequential_beta_spending.R index 26ad6b29..4f5c2077 100644 --- a/tests/testthat/test-f_design_group_sequential_beta_spending.R +++ b/tests/testthat/test-f_design_group_sequential_beta_spending.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_design_group_sequential_beta_spending.R ## | Creation date: 08 November 2023, 09:09:55 -## | 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 Group Sequential Design Functionality with Beta Spending") diff --git a/tests/testthat/test-f_design_plan_plot.R b/tests/testthat/test-f_design_plan_plot.R index 8c0f5e07..25b1141c 100644 --- a/tests/testthat/test-f_design_plan_plot.R +++ b/tests/testthat/test-f_design_plan_plot.R @@ -16,7 +16,7 @@ ## | File name: test-f_design_plan_means.R ## | Creation date: 21 December 2023, 08:52:45 ## | File version: $Revision: 7961 $ -## | Last changed: $Date: 2024-05-30 14:58:05 +0200 (Thu, 30 May 2024) $ +## | Last changed: $Date: 2024-05-30 14:58:05 +0200 (Do, 30 Mai 2024) $ ## | Last changed by: $Author: pahlke $ ## | diff --git a/tests/testthat/test-f_design_utilities.R b/tests/testthat/test-f_design_utilities.R index bf9bbb09..3ea72061 100644 --- a/tests/testthat/test-f_design_utilities.R +++ b/tests/testthat/test-f_design_utilities.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_design_utilities.R ## | Creation date: 08 November 2023, 09:10:53 -## | 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 Design Utility Functions") diff --git a/tests/testthat/test-f_parameter_set_utilities.R b/tests/testthat/test-f_parameter_set_utilities.R index 1de0caff..d16c7109 100644 --- a/tests/testthat/test-f_parameter_set_utilities.R +++ b/tests/testthat/test-f_parameter_set_utilities.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_parameter_set_utilities.R ## | Creation date: 08 November 2023, 09:10:53 -## | 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 Parameter Set Utility Functions") diff --git a/tests/testthat/test-f_simulation_base_means.R b/tests/testthat/test-f_simulation_base_means.R index e0ebc2f9..7add2d2e 100644 --- a/tests/testthat/test-f_simulation_base_means.R +++ b/tests/testthat/test-f_simulation_base_means.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_simulation_base_means.R ## | Creation date: 16 September 2024, 08:44:44 -## | File version: $Revision$ -## | Last changed: $Date$ -## | Last changed by: $Author$ +## | File version: $Revision: 8214 $ +## | Last changed: $Date: 2024-09-16 09:57:16 +0200 (Mo, 16 Sep 2024) $ +## | Last changed by: $Author: pahlke $ ## | test_plan_section("Testing Simulation Means Function") diff --git a/tests/testthat/test-f_simulation_base_rates.R b/tests/testthat/test-f_simulation_base_rates.R index 805d900a..352e295d 100644 --- a/tests/testthat/test-f_simulation_base_rates.R +++ b/tests/testthat/test-f_simulation_base_rates.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_simulation_base_rates.R ## | Creation date: 16 September 2024, 08:44:48 -## | File version: $Revision$ -## | Last changed: $Date$ -## | Last changed by: $Author$ +## | File version: $Revision: 8214 $ +## | Last changed: $Date: 2024-09-16 09:57:16 +0200 (Mo, 16 Sep 2024) $ +## | Last changed by: $Author: pahlke $ ## | test_plan_section("Testing Simulation Rates Function") diff --git a/tests/testthat/test-f_simulation_base_survival.R b/tests/testthat/test-f_simulation_base_survival.R index 823cfc95..a6eee4ba 100644 --- a/tests/testthat/test-f_simulation_base_survival.R +++ b/tests/testthat/test-f_simulation_base_survival.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_simulation_base_survival.R ## | Creation date: 16 September 2024, 08:44:51 -## | File version: $Revision$ -## | Last changed: $Date$ -## | Last changed by: $Author$ +## | File version: $Revision: 8214 $ +## | Last changed: $Date: 2024-09-16 09:57:16 +0200 (Mo, 16 Sep 2024) $ +## | Last changed by: $Author: pahlke $ ## | test_plan_section("Testing Simulation Survival Function") diff --git a/tests/testthat/test-f_simulation_enrichment_means.R b/tests/testthat/test-f_simulation_enrichment_means.R index ae04f2df..d6cc33cb 100644 --- a/tests/testthat/test-f_simulation_enrichment_means.R +++ b/tests/testthat/test-f_simulation_enrichment_means.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_simulation_enrichment_means.R ## | Creation date: 08 November 2023, 09:11:08 -## | 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 Simulation Enrichment Means Function") diff --git a/tests/testthat/test-f_simulation_enrichment_rates.R b/tests/testthat/test-f_simulation_enrichment_rates.R index 64300407..0bff93c5 100644 --- a/tests/testthat/test-f_simulation_enrichment_rates.R +++ b/tests/testthat/test-f_simulation_enrichment_rates.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_simulation_enrichment_rates.R ## | Creation date: 16 September 2024, 09:55:30 -## | File version: $Revision$ -## | Last changed: $Date$ -## | Last changed by: $Author$ +## | File version: $Revision: 8214 $ +## | Last changed: $Date: 2024-09-16 09:57:16 +0200 (Mo, 16 Sep 2024) $ +## | Last changed by: $Author: pahlke $ ## | test_plan_section("Testing Simulation Enrichment Rates Function") diff --git a/tests/testthat/test-f_simulation_enrichment_survival.R b/tests/testthat/test-f_simulation_enrichment_survival.R index 015e9899..0f25511e 100644 --- a/tests/testthat/test-f_simulation_enrichment_survival.R +++ b/tests/testthat/test-f_simulation_enrichment_survival.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_simulation_enrichment_survival.R ## | Creation date: 16 September 2024, 09:45:06 -## | File version: $Revision$ -## | Last changed: $Date$ -## | Last changed by: $Author$ +## | File version: $Revision: 8252 $ +## | Last changed: $Date: 2024-09-23 13:03:24 +0200 (Mo, 23 Sep 2024) $ +## | Last changed by: $Author: pahlke $ ## | 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) ) diff --git a/tests/testthat/test-f_simulation_multiarm_means.R b/tests/testthat/test-f_simulation_multiarm_means.R index 01ab4ae7..1376627e 100644 --- a/tests/testthat/test-f_simulation_multiarm_means.R +++ b/tests/testthat/test-f_simulation_multiarm_means.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_simulation_multiarm_means.R ## | Creation date: 09 February 2024, 10:57:28 -## | File version: $Revision$ -## | Last changed: $Date$ -## | Last changed by: $Author$ +## | File version: $Revision: 7910 $ +## | Last changed: $Date: 2024-05-22 10:02:23 +0200 (Mi, 22 Mai 2024) $ +## | Last changed by: $Author: pahlke $ ## | test_plan_section("Testing Simulation Multi-Arm Means Function") diff --git a/tests/testthat/test-f_simulation_multiarm_rates.R b/tests/testthat/test-f_simulation_multiarm_rates.R index f717787c..2d21fb2d 100644 --- a/tests/testthat/test-f_simulation_multiarm_rates.R +++ b/tests/testthat/test-f_simulation_multiarm_rates.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_simulation_multiarm_rates.R ## | Creation date: 16 September 2024, 09:45:13 -## | File version: $Revision$ -## | Last changed: $Date$ -## | Last changed by: $Author$ +## | File version: $Revision: 8214 $ +## | Last changed: $Date: 2024-09-16 09:57:16 +0200 (Mo, 16 Sep 2024) $ +## | Last changed by: $Author: pahlke $ ## | test_plan_section("Testing Simulation Multi-Arm Rates Function") diff --git a/tests/testthat/test-f_simulation_multiarm_survival.R b/tests/testthat/test-f_simulation_multiarm_survival.R index 299226e2..161df676 100644 --- a/tests/testthat/test-f_simulation_multiarm_survival.R +++ b/tests/testthat/test-f_simulation_multiarm_survival.R @@ -15,9 +15,9 @@ ## | ## | File name: test-f_simulation_multiarm_survival.R ## | Creation date: 12 September 2024, 12:52:12 -## | 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 Simulation Multi-Arm Survival Function") diff --git a/tests/testthat/test-generic_functions.R b/tests/testthat/test-generic_functions.R index ddbdf8b5..ed2ad26b 100644 --- a/tests/testthat/test-generic_functions.R +++ b/tests/testthat/test-generic_functions.R @@ -15,9 +15,9 @@ ## | ## | File name: test-generic_functions.R ## | Creation date: 08 November 2023, 09:12:05 -## | 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 Class 'SummaryFactory'")