Minor improvements

rpact-com · Sep 20, 2024 · 63cda30 · 63cda30
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rpact
 Title: Confirmatory Adaptive Clinical Trial Design and Analysis
-Version: 4.0.1.9259
-Date: 2024-09-19
+Version: 4.0.1.9260
+Date: 2024-09-20
 Authors@R: c(
 	person(
 		given = "Gernot", 

diff --git a/NEWS.md b/NEWS.md
@@ -12,7 +12,7 @@
 * Usage of pipe-operators improved
 * Analysis progress messages are only displayed when R is used interactively
 * Manual use of `kable()` for rpact result objects marked as deprecated, as the formatting and display will be handled automatically by rpact
-* Minor summary improvements
+* The order of all summary entries has been revised and optimized
 * Minimum version of suggested package `ggplot2` changed from 2.2.0 to 3.2.0
 * Issues [#41](https://github.com/rpact-com/rpact/issues/41), [#44](https://github.com/rpact-com/rpact/issues/44), [#46](https://github.com/rpact-com/rpact/issues/46), and [#47](https://github.com/rpact-com/rpact/issues/47) fixed
 * When analyzing with a two-sided test, an issue with the calculation of the conditional rejection probability was fixed

diff --git a/R/class_summary.R b/R/class_summary.R
@@ -13,8 +13,8 @@
 ## |
 ## |  Contact us for information about our services: [email protected]
 ## |
-## |  File version: $Revision: 8240 $
-## |  Last changed: $Date: 2024-09-19 16:58:11 +0200 (Do, 19 Sep 2024) $
+## |  File version: $Revision: 8243 $
+## |  Last changed: $Date: 2024-09-20 07:33:34 +0200 (Fr, 20 Sep 2024) $
 ## |  Last changed by: $Author: pahlke $
 ## |
 
@@ -444,7 +444,8 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
                 formatRepeatedPValues = FALSE,
                 validateParameterType = TRUE,
                 lastStage = NA_integer_,
-                roundDigitsAsInformation = FALSE) {
+                roundDigitsAsInformation = FALSE,
+                showNA = FALSE) {
             if (!is.null(parameterName) && length(parameterName) == 1 &&
                     inherits(parameterSet, "ParameterSet") &&
                     parameterSet$.getParameterType(parameterName) == C_PARAM_NOT_APPLICABLE) {
@@ -584,7 +585,8 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
                     cumsumEnabled = cumsumEnabled,
                     smoothedZeroFormat = smoothedZeroFormat,
                     formatRepeatedPValues = formatRepeatedPValues,
-                    roundDigitsAsInformation = roundDigitsAsInformation
+                    roundDigitsAsInformation = roundDigitsAsInformation,
+                    showNA = showNA
                 )
 
                 if (parameterName1 %in% c("piControl", "overallPiControl", "overallPooledStDevs")) {
@@ -602,7 +604,8 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
                         cumsumEnabled = cumsumEnabled,
                         smoothedZeroFormat = smoothedZeroFormat,
                         formatRepeatedPValues = formatRepeatedPValues,
-                        roundDigitsAsInformation = roundDigitsAsInformation
+                        roundDigitsAsInformation = roundDigitsAsInformation,
+                        showNA = showNA
                     )
                     valuesToShow2 <- self$.getInnerValues(valuesToShow2, transpose = transpose)
                 }
@@ -777,23 +780,31 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
 
                 for (variantIndex in 1:numberOfVariants) {
                     colValues <- self$.getColumnValues(parameterName, values, variantIndex, transposed)
-                    colValues <- .getSummaryValuesFormatted(parameterSet, parameterName1,
-                        colValues,
+                    colValues <- .getSummaryValuesFormatted(
+                        parameterSet, 
+                        parameterName1,
+                        values = colValues,
                         roundDigits = roundDigits,
                         ceilingEnabled = ceilingEnabled, cumsumEnabled = cumsumEnabled,
                         smoothedZeroFormat = smoothedZeroFormat,
                         formatRepeatedPValues = formatRepeatedPValues,
-                        roundDigitsAsInformation = roundDigitsAsInformation
+                        roundDigitsAsInformation = roundDigitsAsInformation,
+                        showNA = showNA
                     )
                     colValues2 <- NA_real_
                     if (!all(is.na(values2))) {
                         colValues2 <- self$.getColumnValues(parameterName, values2, variantIndex, transposed)
-                        colValues2 <- .getSummaryValuesFormatted(parameterSet, parameterName2, colValues2,
-                            roundDigits = roundDigits, ceilingEnabled = ceilingEnabled,
+                        colValues2 <- .getSummaryValuesFormatted(
+                            parameterSet, 
+                            parameterName2, 
+                            values = colValues2,
+                            roundDigits = roundDigits, 
+                            ceilingEnabled = ceilingEnabled,
                             cumsumEnabled = cumsumEnabled,
                             smoothedZeroFormat = smoothedZeroFormat,
                             formatRepeatedPValues = formatRepeatedPValues,
-                            roundDigitsAsInformation = roundDigitsAsInformation
+                            roundDigitsAsInformation = roundDigitsAsInformation,
+                            showNA = showNA
                         )
                     }
                     colValues <- self$.getFormattedParameterValue(valuesToShow = colValues, valuesToShow2 = colValues2)
@@ -923,7 +934,14 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
     )
 )
 
-.formatSummaryValues <- function(values, digits, smoothedZeroFormat = FALSE, formatRepeatedPValues = FALSE) {
+.formatSummaryValues <- function(
+        values, 
+        ...,
+        digits, 
+        smoothedZeroFormat = FALSE, 
+        formatRepeatedPValues = FALSE,
+        showNA = FALSE) {
+
     if (is.na(digits)) {
         digits <- 3
     }
@@ -974,7 +992,8 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
         }
     }
 
-    formattedValue[is.na(formattedValue) | trimws(formattedValue) == "NA"] <- getOption("rpact.summary.na", "")
+    formattedValue[is.na(formattedValue) | trimws(formattedValue) == "NA"] <- 
+        ifelse(showNA, "n/a", getOption("rpact.summary.na", ""))
 
     return(formattedValue)
 }
@@ -989,7 +1008,8 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
         cumsumEnabled = FALSE,
         smoothedZeroFormat = FALSE, 
         formatRepeatedPValues = FALSE,
-        roundDigitsAsInformation = FALSE) {
+        roundDigitsAsInformation = FALSE,
+        showNA = FALSE) {
 
     if (!is.numeric(values)) {
         return(values)
@@ -1048,7 +1068,8 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
                     values <- .formatSummaryValues(values,
                         digits = roundDigits,
                         smoothedZeroFormat = smoothedZeroFormat,
-                        formatRepeatedPValues = formatRepeatedPValues
+                        formatRepeatedPValues = formatRepeatedPValues,
+                        showNA = showNA
                     )
                 }
             },
@@ -3234,7 +3255,7 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
         )
     }
 
-    return(invisible(summaryFactory))
+    return(summaryFactory)
 }
 
 #'
@@ -3576,7 +3597,8 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
             parameterName = parameterNameSubjects,
             parameterCaption = subjectsCaption, 
             roundDigits = digitSettings$digitsSampleSize,
-            validateParameterType = !countDataEnabled
+            validateParameterType = !countDataEnabled,
+            showNA = TRUE
         )
     }
 

diff --git a/R/f_simulation_base_count_data.R b/R/f_simulation_base_count_data.R
@@ -13,8 +13,8 @@
 ## |
 ## |  Contact us for information about our services: [email protected]
 ## |
-## |  File version: $Revision: 8241 $
-## |  Last changed: $Date: 2024-09-19 17:11:12 +0200 (Do, 19 Sep 2024) $
+## |  File version: $Revision: 8243 $
+## |  Last changed: $Date: 2024-09-20 07:33:34 +0200 (Fr, 20 Sep 2024) $
 ## |  Last changed by: $Author: pahlke $
 ## |
 
@@ -126,21 +126,22 @@
 #' \enumerate{
 #'   \item \code{iterationNumber}: The number of the simulation iteration.
 #'   \item \code{stageNumber}: The stage.
-#'   \item \code{lambda1}: The assumed or derived event rate in the treatment group (if available).
-#'   \item \code{lambda2}: The assumed or derived event rate in the control group (if available).
-#'   \item \code{numberOfSubjects}: The number of subjects under consideration when the
-#'         (interim) analysis takes place.
+#'   \item \code{lambda1}: The assumed or derived event rate in the treatment group.
+#'   \item \code{lambda2}: The assumed or derived event rate in the control group.
+#'   \item \code{accrualTime}: The assumed accrualTime.
+#'   \item \code{followUpTime}: The  assumed followUpTime.
+#'   \item \code{overdispersion}: The  assumed overdispersion.
+#'   \item \code{fixedFollowUp}: The  assumed fixedFollowUp.
+#'   \item \code{numberOfSubjects}: The number of subjects under consideration when the (interim) analysis takes place.
 #'   \item \code{rejectPerStage}: 1 if null hypothesis can be rejected, 0 otherwise.
 #'   \item \code{futilityPerStage}: 1 if study should be stopped for futility, 0 otherwise.
 #'   \item \code{testStatistic}: The test statistic that is used for the test decision
-#'   \item \code{overallLambda1}: The cumulative rate in treatment group 1.
-#'   \item \code{overallLambda2}: The cumulative rate in treatment group 2.
-#'   \item \code{sampleSizesPerStage1}: The stage-wise sample size in treatment group 1.
-#'   \item \code{sampleSizesPerStage2}: The stage-wise sample size in treatment group 2.
+#'   \item \code{estimatedLambda1}: The estimated rate in treatment group 1.
+#'   \item \code{estimatedLambda2}: The estimated rate in treatment group 2.
+#'   \item \code{estimatedOverdispersion}: The estimated overdispersion.
+#'   \item \code{infoAnalysis}: The Fisher information at interim stage.
 #'   \item \code{trialStop}: \code{TRUE} if study should be stopped for efficacy or futility or final stage, \code{FALSE} otherwise.
-#'   \item \code{conditionalPowerAchieved}: The conditional power for the subsequent stage of the trial for
-#'         selected sample size and effect. The effect is either estimated from the data or can be
-#'         user defined with \code{lambda1H1} and \code{lambda2H1}.
+#'   \item \code{conditionalPowerAchieved}: Not yet available
 #' }
 #'
 #' @template return_object_simulation_results
@@ -312,6 +313,9 @@ getSimulationCounts <- function(design = NULL,
     dataTestStatistic <- rep(NA_real_, len)
     dataTrialStop <- rep(NA, len)
     dataConditionalPower <- rep(NA_real_, len)
+    dataSampleSizes <- rep(NA_real_, len)
+    dataReject <- rep(0, len)
+    dataFutility <- rep(0, len)
 
     index <- 1
     messageShown <- FALSE
@@ -411,6 +415,7 @@ getSimulationCounts <- function(design = NULL,
                 zValue <- (2 * directionUpper - 1) * (log(nb[1]) - log(nb[2]) - log(thetaH0)) * sqrt(infoAnalysis)
                 if (!is.na(zValue) && zValue > .getCriticalValues(design, 1)) {
                     reject[1] <- reject[1] + 1
+                    dataReject[index] <- 1
                 }
                 iterations[1, iCase] <- iterations[1, iCase] + 1
                 nTotal <- nTotal + n1 + n2
@@ -423,14 +428,15 @@ getSimulationCounts <- function(design = NULL,
                 dataLambda1[index] <- lambda1[iCase]
                 dataLambda2[index] <- lambda2
                 dataOverdispersion[index] <- overdispersion
-                dataFixedFollowUp[index] <- !is.na(fixedExposureTime)
+                dataFixedFollowUp[index] <- fixedExposureTime
                 dataNegativeBinomialEstimate1[index] <- nb[1]
                 dataNegativeBinomialEstimate2[index] <- nb[2]
                 dataNegativeBinomialOverdispersion[index] <- nb[3]
                 dataInfoAnalysis[index] <- infoAnalysis
                 dataTestStatistic[index] <- zValue
                 dataTrialStop[index] <- TRUE
                 dataConditionalPower[index] <- NA_real_
+                dataSampleSizes[index] <- n1 + n2
 
                 index <- index + 1
             } else {
@@ -507,25 +513,28 @@ getSimulationCounts <- function(design = NULL,
                     dataLambda1[index] <- lambda1[iCase]
                     dataLambda2[index] <- lambda2
                     dataOverdispersion[index] <- overdispersion
-                    dataFixedFollowUp[index] <- !is.na(fixedExposureTime)
+                    dataFixedFollowUp[index] <- fixedExposureTime
                     dataNegativeBinomialEstimate1[index] <- nb[1]
                     dataNegativeBinomialEstimate2[index] <- nb[2]
                     dataNegativeBinomialOverdispersion[index] <- nb[3]
                     dataInfoAnalysis[index] <- infoAnalysis
                     dataTestStatistic[index] <- zValue
                     dataConditionalPower[index] <- conditionalPowerAchieved
                     dataTrialStop[index] <- FALSE
+                    dataSampleSizes[index] <- length(timeUnderObservation1) + length(timeUnderObservation2)
 
                     if (!is.na(zValue)) {
                         if (zValue > .getCriticalValues(design, k)) {
                             reject[k] <- reject[k] + 1
                             dataTrialStop[index] <- TRUE
+                            dataReject[index] <- 1
                             index <- index + 1
                             break
                         }
                         if (zValue < design$futilityBounds[k] && k < kMax) {
                             futility[k] <- futility[k] + 1
                             dataTrialStop[index] <- TRUE
+                            dataFutility[index] <- 1
                             index <- index + 1
                             break
                         }
@@ -584,6 +593,7 @@ getSimulationCounts <- function(design = NULL,
     simulationResults$iterations <- iterations
     simulationResults$.setParameterType("iterations", C_PARAM_GENERATED)
 
+    sampleSizePerStage[is.nan(sampleSizePerStage)] <- NA_integer_
     simulationResults$numberOfSubjects <- sampleSizePerStage
     simulationResults$.setParameterType(
         "numberOfSubjects",
@@ -615,20 +625,22 @@ getSimulationCounts <- function(design = NULL,
     }
 
     data <- data.frame(
-        caseNumber = dataCase,
         iterationNumber = dataIterationNumber,
         stageNumber = dataStageNumber,
-        accrualTime = dataAccrualTime,
-        followUpTime = dataFollowUpTime,
         lambda1 = dataLambda1,
         lambda2 = dataLambda2,
         overdispersion = dataOverdispersion,
+        accrualTime = dataAccrualTime,
+        followUpTime = dataFollowUpTime,
         fixedFollowUp = dataFixedFollowUp,
-        negativeBinomialEstimate1 = dataNegativeBinomialEstimate1,
-        negativeBinomialEstimate2 = dataNegativeBinomialEstimate2,
-        nbOverdispersion = dataNegativeBinomialOverdispersion,
-        infoAnalysis = dataInfoAnalysis,
+        numberOfSubjects = dataSampleSizes,
+        rejectPerStage = dataReject,
+        futilityPerStage = dataFutility,
         testStatistic = dataTestStatistic,
+        estimatedLambda1 = dataNegativeBinomialEstimate1,
+        estimatedLambda2 = dataNegativeBinomialEstimate2,
+        estimatedOverdispersion = dataNegativeBinomialOverdispersion,
+        infoAnalysis = dataInfoAnalysis,
         trialStop = dataTrialStop,
         conditionalPowerAchieved = dataConditionalPower
     )

diff --git a/man-roxygen/examples_get_simulation_counts.R b/man-roxygen/examples_get_simulation_counts.R
@@ -18,19 +18,19 @@
 #' # equidistant time points (lambda1, lambda2, and overdispersion as specified,
 #' # no futility stopping):
 #' dOF <- getDesignGroupSequential(
-#'     kMax = 3, 
-#'     alpha = 0.025, 
-#'     beta = 0.2, 
+#'     kMax = 3,
+#'     alpha = 0.025,
+#'     beta = 0.2,
 #'     typeOfDesign = "asOF")
-#'
+#' 
 #' getSimulationCounts(design = dOF,
-#'     lambda1 = seq(0.04, 0.12, 0.02), 
-#'     lambda2 = 0.12, 
-#'     directionUpper = FALSE,       
-#'     overdispersion = 5, 
+#'     lambda1 = seq(0.04, 0.12, 0.02),
+#'     lambda2 = 0.12,
+#'     directionUpper = FALSE,
+#'     overdispersion = 5,
 #'     plannedCalendarTime = (1:3)/3*4,
-#'     maxNumberOfSubjects = 264, 
-#'     followUpTime = 2.75, 
+#'     maxNumberOfSubjects = 264,
+#'     followUpTime = 2.75,
 #'     accrualTime = 1.25,
 #'     maxNumberOfIterations = 1000)
 #' }