Merge pull request #59 from rpact-com/dev/4.0.1

rpact-com · Sep 27, 2024 · 1bcaa28 · 1bcaa28
2 parents 13728e3 + 6abbd4a
commit 1bcaa28
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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: 4.0.1.9264
-Date: 2024-09-26
+Version: 4.1.0
+Date: 2024-09-27
 Authors@R: c(
 	person(
 		given = "Gernot", 

diff --git a/R/class_simulation_results.R b/R/class_simulation_results.R
@@ -13,8 +13,8 @@
 ## |
 ## |  Contact us for information about our services: [email protected]
 ## |
-## |  File version: $Revision: 8232 $
-## |  Last changed: $Date: 2024-09-19 08:22:37 +0200 (Do, 19 Sep 2024) $
+## |  File version: $Revision: 8277 $
+## |  Last changed: $Date: 2024-09-27 08:16:45 +0200 (Fr, 27 Sep 2024) $
 ## |  Last changed by: $Author: pahlke $
 ## |
 
@@ -567,6 +567,9 @@ SimulationResults <- R6::R6Class("SimulationResults",
                 "numberOfPopulations",
                 "expectedNumberOfSubjects",
                 "expectedNumberOfEvents",
+                "numberOfSubjects",
+                "numberOfSubjects1",
+                "numberOfSubjects2",
                 "sampleSizes",
                 "singleEventsPerArmAndStage",
                 "singleEventsPerSubsetAndStage",
@@ -1708,10 +1711,10 @@ SimulationResultsCountData <- R6::R6Class("SimulationResultsCountData",
         accrualIntensity = NULL,
         followUpTime = NULL,
         groups = NULL,
+        expectedNumberOfSubjects = NULL,
         numberOfSubjects = NULL,
         numberOfSubjects1 = NULL,
         numberOfSubjects2 = NULL,
-        expectedNumberOfSubjects = NULL,
         iterations = NULL,
         futilityStop = NULL,
         futilityPerStage = NULL,

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: 8276 $
-## |  Last changed: $Date: 2024-09-26 13:37:54 +0200 (Do, 26 Sep 2024) $
+## |  File version: $Revision: 8277 $
+## |  Last changed: $Date: 2024-09-27 08:16:45 +0200 (Fr, 27 Sep 2024) $
 ## |  Last changed by: $Author: pahlke $
 ## |
 
@@ -506,7 +506,8 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
                                 "expectedEventsH1", 
                                 "expectedNumberOfEvents", 
                                 "expectedStudyDurationH1",
-                                "studyDuration")) {
+                                "studyDuration",
+                                "earlyStop")) {
                             transposed <- TRUE
                         }
                     }
@@ -3552,8 +3553,9 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
         }
 
         if (designPlan$.getParameterType(parameterNameSubjects) == C_PARAM_GENERATED) {
-            subjectsCaption <- ifelse(design$kMax > 1 && inherits(designPlan, "SimulationResults") &&
-                    !survivalEnabled, "Stage-wise number of subjects", "Number of subjects")
+            subjectsCaption <- ifelse(design$kMax > 1 && 
+                    inherits(designPlan, "SimulationResults") && !survivalEnabled, 
+                    "Stage-wise number of subjects", "Number of subjects")
             summaryFactory$addParameter(designPlan,
                 parameterName = parameterNameSubjects,
                 parameterCaption = subjectsCaption,
@@ -3566,33 +3568,6 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
         }
     }
 
-    if (baseEnabled && countDataEnabled && design$kMax > 1 &&
-        !is.null(designPlan[["maxNumberOfSubjects"]]) &&
-        designPlan$.getParameterType("maxNumberOfSubjects") == C_PARAM_GENERATED) {
-        summaryFactory$addParameter(designPlan,
-            parameterName = "maxNumberOfSubjects",
-            parameterCaption = "Maximum number of subjects",
-            roundDigits = digitSettings$digitsSampleSize
-        )
-        summaryFactory$addParameter(designPlan,
-            parameterName = "expectedNumberOfSubjectsH1", 
-            parameterCaption = "Expected number of subjects",
-            roundDigits = digitSettings$digitsSampleSize
-        )
-    }
-    if (baseEnabled && !countDataEnabled && design$kMax > 1) {
-        summaryFactory$addParameter(designPlan,
-            parameterName = ifelse(inherits(designPlan, "TrialDesignPlan") &&
-                    (designPlan$.isSampleSizeObject() || countDataEnabled),
-                "expectedNumberOfSubjectsH1", "expectedNumberOfSubjects"), 
-            parameterCaption = "Expected number of subjects under H1",
-            roundDigits = digitSettings$digitsSampleSize,
-            transpose = TRUE,
-            validateParameterType = !countDataEnabled,
-            lastStage = design$kMax
-        )
-    }
-
     if (simulationEnabled && (multiArmEnabled || enrichmentEnabled || countDataEnabled)) {
         if (survivalEnabled) {
             summaryFactory$addParameter(designPlan,
@@ -3612,6 +3587,29 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
             )
         }
     }
+    else if (baseEnabled && design$kMax > 1) {
+        parameterName <- ifelse(inherits(designPlan, "TrialDesignPlan") &&
+            (designPlan$.isSampleSizeObject() || countDataEnabled),
+            "expectedNumberOfSubjectsH1", "expectedNumberOfSubjects") 
+        summaryFactory$addParameter(designPlan,
+            parameterName = parameterName, 
+            parameterCaption = "Expected number of subjects under H1",
+            roundDigits = digitSettings$digitsSampleSize,
+            transpose = TRUE,
+            validateParameterType = !countDataEnabled,
+            lastStage = design$kMax
+        )
+        if (countDataEnabled &&
+                (is.null(designPlan[[parameterName]]) || all(is.na(designPlan[[parameterName]]))) &&
+                !is.null(designPlan[["maxNumberOfSubjects"]]) &&
+                designPlan$.getParameterType("maxNumberOfSubjects") == C_PARAM_GENERATED) {
+            summaryFactory$addParameter(designPlan,
+                parameterName = "maxNumberOfSubjects",
+                parameterCaption = "Maximum number of subjects",
+                roundDigits = digitSettings$digitsSampleSize
+            )
+        }
+    }
 
     if (baseEnabled && survivalEnabled && outputSize %in% c("medium", "large")) {
         parameterNameEvents <- NULL
@@ -3671,7 +3669,8 @@ SummaryFactory <- R6::R6Class("SummaryFactory",
             parameterCaption = "Overall exit probability", # (under H1)
             roundDigits = digitSettings$digitsProbabilities,
             smoothedZeroFormat = TRUE,
-            transpose = TRUE
+            transpose = TRUE,
+            lastStage = design$kMax 
         )
     }
 

diff --git a/R/f_design_plan_count_data.R b/R/f_design_plan_count_data.R
@@ -13,8 +13,8 @@
 ## |
 ## |  Contact us for information about our services: [email protected]
 ## |
-## |  File version: $Revision: 8268 $
-## |  Last changed: $Date: 2024-09-25 16:14:45 +0200 (Mi, 25 Sep 2024) $
+## |  File version: $Revision: 8279 $
+## |  Last changed: $Date: 2024-09-27 10:49:35 +0200 (Fr, 27 Sep 2024) $
 ## |  Last changed by: $Author: wassmer $
 ## |
 
@@ -162,7 +162,7 @@
         followUpTime <- studyTime - max(accrualTime)
     }
 
-    if (designPlan$.objectType == "power"){
+    if (designPlan$.objectType == "power") {
         nParameters <- 1
     } else {
         nParameters <- length(lambda1)
@@ -192,7 +192,7 @@
     criticalValues <- .getCriticalValues(design)
     futilityBounds <- design$futilityBounds
     futilityBounds[!is.na(futilityBounds) & futilityBounds <= C_FUTILITY_BOUNDS_DEFAULT] <- NA_real_
-    
+
     for (iCase in 1:nParameters) {
         ar <- allocationRatioPlanned[iCase]
 
@@ -224,7 +224,7 @@
                 recruit2 <- seq(0, accrualTime, length.out = maxNumberOfSubjects[iCase] / (1 + ar))
             }
         }
-        
+
         # calculate theta that solves (ln(theta) - ln(thetaH0) sqrt(FisherInformation_k) = boundary
         for (j in seq_len(length(criticalValues))) {
             if (all(is.na(numberOfSubjects[, iCase]))) {
@@ -354,12 +354,13 @@
             )$root)
         },
         error = function(e) {
-            stop("Failed to calculate the calendar time. ",
+            warning("Failed to calculate the calendar time. ",
                 "Fisher information might be bounded, e.g., due to overdispersion > 0",
                 call. = FALSE
             )
         }
     )
+    return(NA_real_)
 }
 
 .getMaximumSampleSizeTwoGroups <- function(allocationRatioPlanned,
@@ -402,8 +403,7 @@
     ))
 }
 
-.getDesignPlanCountData <- function(
-        design,
+.getDesignPlanCountData <- function(design,
         designCharacteristics,
         objectType,
         sided,
@@ -1137,7 +1137,9 @@ getPowerCounts <- function(design = NULL, ...,
         accrualTime <- accrualTime[-1]
     }
     directionUpper <- .assertIsValidDirectionUpper(directionUpper,
-        design, objectType = "power", userFunctionCallEnabled = TRUE)
+        design,
+        objectType = "power", userFunctionCallEnabled = TRUE
+    )
     .setValueAndParameterType(designPlan, "directionUpper", directionUpper, C_DIRECTION_UPPER_DEFAULT)
 
     futilityPerStage <- matrix(NA_real_, kMax - 1, totalCases)

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: 8243 $
-## |  Last changed: $Date: 2024-09-20 07:33:34 +0200 (Fr, 20 Sep 2024) $
+## |  File version: $Revision: 8277 $
+## |  Last changed: $Date: 2024-09-27 08:16:45 +0200 (Fr, 27 Sep 2024) $
 ## |  Last changed by: $Author: pahlke $
 ## |
 
@@ -593,27 +593,33 @@ getSimulationCounts <- function(design = NULL,
     simulationResults$iterations <- iterations
     simulationResults$.setParameterType("iterations", C_PARAM_GENERATED)
 
+    if (kMax == 1) {
+        sampleSizePerStage <- rep(maxNumberOfSubjects, totalCases)
+        expectedSampleSize <- sampleSizePerStage
+    }
+
     sampleSizePerStage[is.nan(sampleSizePerStage)] <- NA_integer_
     simulationResults$numberOfSubjects <- sampleSizePerStage
     simulationResults$.setParameterType(
         "numberOfSubjects",
-        ifelse(is.na(nTotal), C_PARAM_NOT_APPLICABLE, C_PARAM_GENERATED)
+        ifelse(kMax == 1 || is.na(nTotal), C_PARAM_NOT_APPLICABLE, C_PARAM_GENERATED)
     )
+
     simulationResults$expectedNumberOfSubjects <- expectedSampleSize
     simulationResults$.setParameterType(
         "expectedNumberOfSubjects",
-        ifelse(all(is.na(expectedSampleSize)), C_PARAM_NOT_APPLICABLE, C_PARAM_GENERATED)
+        ifelse(kMax == 1 || all(is.na(expectedSampleSize)), C_PARAM_NOT_APPLICABLE, C_PARAM_GENERATED)
     )
 
     simulationResults$numberOfSubjects1 <- n1
     simulationResults$.setParameterType(
         "numberOfSubjects1",
-        ifelse(allocationRatioPlanned == 1, C_PARAM_NOT_APPLICABLE, C_PARAM_GENERATED)
+        ifelse(kMax == 1 && allocationRatioPlanned != 1, C_PARAM_GENERATED, C_PARAM_NOT_APPLICABLE)
     )
     simulationResults$numberOfSubjects2 <- n2
     simulationResults$.setParameterType(
         "numberOfSubjects2",
-        ifelse(allocationRatioPlanned == 1, C_PARAM_NOT_APPLICABLE, C_PARAM_GENERATED)
+        ifelse(kMax == 1 && allocationRatioPlanned != 1, C_PARAM_GENERATED, C_PARAM_NOT_APPLICABLE)
     )
 
     simulationResults$overallReject <- overallReject

diff --git a/cran-comments.md b/cran-comments.md
@@ -10,7 +10,7 @@ There were no ERRORs or WARNINGs.
 
 ## Unit tests: testthat results (complete test)
 
-OK:       36947
+OK:       36943
 Failed:   0
 Warnings: 0
 Skipped:  0
diff --git a/inst/doc/rpact_getting_started.html b/inst/doc/rpact_getting_started.html
@@ -12,7 +12,7 @@
 
 <meta name="author" content="Friedrich Pahlke and Gernot Wassmer" />
 
-<meta name="date" content="2024-09-26" />
+<meta name="date" content="2024-09-27" />
 
 <title>Getting started with rpact</title>
 
@@ -239,7 +239,7 @@
 
 <h1 class="title toc-ignore">Getting started with rpact</h1>
 <h4 class="author">Friedrich Pahlke and Gernot Wassmer</h4>
-<h4 class="date">2024-09-26</h4>
+<h4 class="date">2024-09-27</h4>
 
 
 

diff --git a/tests/testthat/test-f_design_plan_count_data.R b/tests/testthat/test-f_design_plan_count_data.R
@@ -178,7 +178,6 @@ test_that("'getSampleSizeCounts': Sample size calculation of testing count data
         lambda2 = 1.4, accrualTime = c(0, 20), allocationRatioPlanned = 1, maxNumberOfSubjects = 100
     )
 
-
     ## Comparison of the results of TrialDesignPlanCountData object 'result4' with expected results
     expect_equal(result4$directionUpper, c(FALSE, FALSE, FALSE), label = paste0(result4$directionUpper))
     expect_equal(result4$theta, c(0.75, 0.85714286, 0.96428571), tolerance = 1e-07, label = paste0(result4$theta))
@@ -214,10 +213,11 @@ test_that("'getSampleSizeCounts': Sample size calculation of testing count data
         expect_true(is.matrix(mtx))
         expect_true(nrow(mtx) > 0 && ncol(mtx) > 0)
     }
+
     # @refFS[Formula]{fs:FisherInfCounts}
     # @refFS[Formula]{fs:maximumSampleSizeVariableExposureCounts}
     # @refFS[Formula]{fs:observationTimePerStageCounts}
-    expect_error(getSampleSizeCounts(
+    expect_warning(getSampleSizeCounts(
         alpha = 0.01, beta = 0.05, lambda1 = seq(1.35, 1.35, 0.15),
         overdispersion = 0.01, lambda2 = 1.4, accrualTime = c(0, 10, 20), accrualIntensity = c(5, 10)
     ))

diff --git a/tests/testthat/test-f_simulation_base_count_data.R b/tests/testthat/test-f_simulation_base_count_data.R
@@ -269,21 +269,17 @@ test_that("'getSimulationCounts': fixed exposure", {
 
     ## Comparison of the results of SimulationResultsCountData object 'result2' with expected results
     expect_equal(result2$lambda1, c(1.05, 1.5866662), tolerance = 1e-07, label = paste0(result2$lambda1))
-    expect_equal(result2$numberOfSubjects[1, ], c(0, 0), label = paste0(result2$numberOfSubjects[1, ]))
     expect_equal(result2$iterations[1, ], c(100, 100), label = paste0(result2$iterations[1, ]))
     expect_equal(result2$overallReject, c(0.14, 0), tolerance = 1e-07, label = paste0(result2$overallReject))
-    expect_equal(result2$expectedNumberOfSubjects, c(0, 0), label = paste0(result2$expectedNumberOfSubjects))
     if (isTRUE(.isCompleteUnitTestSetEnabled())) {
         invisible(capture.output(expect_error(print(result2), NA)))
         expect_output(print(result2)$show())
         invisible(capture.output(expect_error(summary(result2), NA)))
         expect_output(summary(result2)$show())
         suppressWarnings(result2CodeBased <- eval(parse(text = getObjectRCode(result2, stringWrapParagraphWidth = NULL))))
         expect_equal(result2CodeBased$lambda1, result2$lambda1, tolerance = 1e-07)
-        expect_equal(result2CodeBased$numberOfSubjects, result2$numberOfSubjects, tolerance = 1e-07)
         expect_equal(result2CodeBased$iterations, result2$iterations, tolerance = 1e-07)
         expect_equal(result2CodeBased$overallReject, result2$overallReject, tolerance = 1e-07)
-        expect_equal(result2CodeBased$expectedNumberOfSubjects, result2$expectedNumberOfSubjects, tolerance = 1e-07)
         expect_type(names(result2), "character")
         df <- as.data.frame(result2)
         expect_s3_class(df, "data.frame")