diff --git a/DESCRIPTION b/DESCRIPTION
index 3b0e2f0..73d0171 100644
--- 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
index c254783..4d22bab 100644
--- a/R/class_simulation_results.R
+++ b/R/class_simulation_results.R
@@ -13,8 +13,8 @@
## |
## | Contact us for information about our services: info@rpact.com
## |
-## | 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
index 63aebf6..369e53b 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: 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
index c97a0d0..d68d290 100644
--- 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: info@rpact.com
## |
-## | 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
index e8f78a7..24f3107 100644
--- 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: info@rpact.com
## |
-## | 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$overallReject <- overallReject
diff --git a/cran-comments.md b/cran-comments.md
index 531380c..2ff0769 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -10,7 +10,7 @@ There were no ERRORs or WARNINGs.
## Unit tests: testthat results (complete test)
-OK: 36947
+OK: 36943
Failed: 0
Warnings: 0
Skipped: 0
diff --git a/inst/doc/rpact_getting_started.html b/inst/doc/rpact_getting_started.html
index 5578db4..a79f378 100644
--- a/inst/doc/rpact_getting_started.html
+++ b/inst/doc/rpact_getting_started.html
@@ -12,7 +12,7 @@
-
+
Getting started with rpact
@@ -239,7 +239,7 @@
Getting started with rpact
Friedrich Pahlke and Gernot Wassmer
-2024-09-26
+2024-09-27
diff --git a/tests/testthat/test-f_design_plan_count_data.R b/tests/testthat/test-f_design_plan_count_data.R
index 43b0b36..fdcce4f 100644
--- a/tests/testthat/test-f_design_plan_count_data.R
+++ b/tests/testthat/test-f_design_plan_count_data.R
@@ -178,7 +178,6 @@ test_that("'getSampleSizeCounts': Sample size calculation of testing count data
lambda2 = 1.4, accrualTime = c(0, 20), allocationRatioPlanned = 1, maxNumberOfSubjects = 100
)
-
## Comparison of the results of TrialDesignPlanCountData object 'result4' with expected results
expect_equal(result4$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$theta))
@@ -214,10 +213,11 @@ test_that("'getSampleSizeCounts': Sample size calculation of testing count data
expect_true(is.matrix(mtx))
expect_true(nrow(mtx) > 0 && ncol(mtx) > 0)
}
+
# @refFS[Formula]{fs:FisherInfCounts}
# @refFS[Formula]{fs:maximumSampleSizeVariableExposureCounts}
# @refFS[Formula]{fs:observationTimePerStageCounts}
- expect_error(getSampleSizeCounts(
+ expect_warning(getSampleSizeCounts(
alpha = 0.01, beta = 0.05, lambda1 = seq(1.35, 1.35, 0.15),
overdispersion = 0.01, lambda2 = 1.4, accrualTime = c(0, 10, 20), accrualIntensity = c(5, 10)
))
diff --git a/tests/testthat/test-f_simulation_base_count_data.R b/tests/testthat/test-f_simulation_base_count_data.R
index 8c187eb..d34a536 100644
--- a/tests/testthat/test-f_simulation_base_count_data.R
+++ b/tests/testthat/test-f_simulation_base_count_data.R
@@ -269,10 +269,8 @@ test_that("'getSimulationCounts': fixed exposure", {
## Comparison of the results of SimulationResultsCountData object 'result2' with expected results
expect_equal(result2$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())
@@ -280,10 +278,8 @@ test_that("'getSimulationCounts': fixed exposure", {
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")