CRAN release of rpact version 3.3.2

rpact-com · Nov 7, 2022 · c314850 · c314850
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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: 3.3.1
-Date: 2022-08-24
+Version: 3.3.2
+Date: 2022-11-04
 Authors@R: c(
 	person(
 		given = "Gernot", 
@@ -18,81 +18,52 @@ Description: Design and analysis of confirmatory adaptive clinical trials with c
 License: LGPL-3
 Encoding: UTF-8
 LazyData: true
-URL: https://www.rpact.org, https://www.rpact.com, https://github.com/rpact-com/rpact
+URL: https://www.rpact.org, https://www.rpact.com,
+        https://github.com/rpact-com/rpact
 BugReports: https://github.com/rpact-com/rpact/issues
 Language: en-US
-Depends: 
-	R (>= 3.5.0)
-Imports:
-	methods,
-	stats,
-	utils,
-	graphics,
-	tools,
-	Rcpp (>= 1.0.0)
+Depends: R (>= 3.5.0)
+Imports: methods, stats, utils, graphics, tools, Rcpp (>= 1.0.3)
 LinkingTo: Rcpp
-Suggests: 
-	parallel,
-	ggplot2 (>= 2.2.0),	
-	testthat (>= 2.0.0),
-	mnormt (>= 1.5-7),
-	knitr (>= 1.19), 
-	rmarkdown (>= 1.10)
+SystemRequirements: C++11
+Suggests: parallel, ggplot2 (>= 2.2.0), testthat (>= 3.0.0), mnormt (>=
+        1.5-7), knitr (>= 1.19), rmarkdown (>= 1.10)
 VignetteBuilder: knitr, rmarkdown
 RoxygenNote: 7.2.1
 Config/testthat/edition: 3
-Collate: 
-    'RcppExports.R'
-    'f_logger.R'
-    'f_core_constants.R'
-    'f_core_utilities.R'
-    'f_core_assertions.R'
-    'f_analysis_utilities.R'
-    'f_parameter_set_utilities.R'
-    'class_core_parameter_set.R'
-    'class_core_plot_settings.R'
-    'f_analysis_base.R'
-    'class_analysis_dataset.R'
-    'f_core_plot.R'
-    'class_design.R'
-    'class_analysis_stage_results.R'
-    'class_analysis_results.R'
-    'class_time.R'
-    'class_design_set.R'
-    'f_design_utilities.R'
-    'class_design_plan.R'
-    'class_design_power_and_asn.R'
-    'class_event_probabilities.R'
-    'f_simulation_utilities.R'
-    'f_simulation_base_survival.R'
-    'class_simulation_results.R'
-    'class_summary.R'
-    'data.R'
-    'f_analysis_base_means.R'
-    'f_analysis_base_rates.R'
-    'f_analysis_base_survival.R'
-    'f_analysis_enrichment.R'
-    'f_analysis_enrichment_means.R'
-    'f_analysis_enrichment_rates.R'
-    'f_analysis_enrichment_survival.R'
-    'f_analysis_multiarm.R'
-    'f_analysis_multiarm_means.R'
-    'f_analysis_multiarm_rates.R'
-    'f_analysis_multiarm_survival.R'
-    'f_core_output_formats.R'
-    'f_design_fisher_combination_test.R'
-    'f_design_group_sequential.R'
-    'f_design_sample_size_calculator.R'
-    'f_quality_assurance.R'
-    'f_simulation_base_means.R'
-    'f_simulation_base_rates.R'
-    'f_simulation_enrichment.R'
-    'f_simulation_enrichment_means.R'
-    'f_simulation_enrichment_rates.R'
-    'f_simulation_enrichment_survival.R'
-    'f_simulation_multiarm.R'
-    'f_simulation_multiarm_means.R'
-    'f_simulation_multiarm_rates.R'
-    'f_simulation_multiarm_survival.R'
-    'parameter_descriptions.R'
-    'pkgname.R'
+Config/testthat/parallel: true
+Config/testthat/start-first: *analysis*
+Collate: 'RcppExports.R' 'f_logger.R' 'f_core_constants.R'
+        'f_core_utilities.R' 'f_core_assertions.R'
+        'f_analysis_utilities.R' 'f_parameter_set_utilities.R'
+        'class_core_parameter_set.R' 'class_core_plot_settings.R'
+        'f_core_plot.R' 'class_design.R' 'f_analysis_base.R'
+        'class_analysis_dataset.R' 'class_analysis_stage_results.R'
+        'class_analysis_results.R' 'class_time.R' 'class_design_set.R'
+        'f_design_utilities.R' 'class_design_plan.R'
+        'class_design_power_and_asn.R' 'class_event_probabilities.R'
+        'f_simulation_utilities.R' 'f_simulation_base_survival.R'
+        'class_simulation_results.R' 'class_summary.R' 'data.R'
+        'f_analysis_base_means.R' 'f_analysis_base_rates.R'
+        'f_analysis_base_survival.R' 'f_analysis_enrichment.R'
+        'f_analysis_enrichment_means.R' 'f_analysis_enrichment_rates.R'
+        'f_analysis_enrichment_survival.R' 'f_analysis_multiarm.R'
+        'f_analysis_multiarm_means.R' 'f_analysis_multiarm_rates.R'
+        'f_analysis_multiarm_survival.R' 'f_core_output_formats.R'
+        'f_design_fisher_combination_test.R'
+        'f_design_group_sequential.R'
+        'f_design_sample_size_calculator.R' 'f_quality_assurance.R'
+        'f_simulation_base_means.R' 'f_simulation_base_rates.R'
+        'f_simulation_enrichment.R' 'f_simulation_enrichment_means.R'
+        'f_simulation_enrichment_rates.R'
+        'f_simulation_enrichment_survival.R' 'f_simulation_multiarm.R'
+        'f_simulation_multiarm_means.R' 'f_simulation_multiarm_rates.R'
+        'f_simulation_multiarm_survival.R' 'parameter_descriptions.R'
+        'pkgname.R'
+NeedsCompilation: yes
+Packaged: 2022-11-04 10:37:32 UTC; fried
+Author: Gernot Wassmer [aut],
+  Friedrich Pahlke [aut, cre]
+Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>
+Repository: CRAN
+Date/Publication: 2022-11-04 15:30:21 UTC
diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,13 @@
 
+# rpact 3.3.2
+
+* Design objects can be piped into `getDataset()` to enable pipe syntax for analysis, e.g., 
+`getDesignGroupSequential() |> getDataset(dataMeans) |> getAnalysisResults()`
+* Performance of simulation means improved for 1 and 2 groups (by translating from R to C++)
+* Total test time was cut in half by improving simulation performance and enabling parallel testing
+* `SystemRequirements: C++11` added to DESCRIPTION to enable C++ 11 compilation on R 3.x
+* Minor improvements
+
 # rpact 3.3.1
 
 * Help pages improved

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -57,6 +57,10 @@ getDesignGroupSequentialUserDefinedBetaSpendingCpp <- function(criticalValues, k
     .Call(`_rpact_getDesignGroupSequentialUserDefinedBetaSpendingCpp`, criticalValues, kMax, userAlphaSpending, userBetaSpending, sided, informationRates, bindingFutility, tolerance, typeOfDesign, gammaA, alpha, betaAdjustment, twoSidedPower)
 }
 
+getSimulationMeansLoopCpp <- function(alternative, kMax, maxNumberOfIterations, designNumber, informationRates, futilityBounds, alpha0Vec, criticalValues, meanRatio, thetaH0, stDev, groups, normalApproximation, plannedSubjects, directionUpper, allocationRatioPlanned, minNumberOfSubjectsPerStage, maxNumberOfSubjectsPerStage, conditionalPower, thetaH1, stDevH1, calcSubjectsFunction) {
+    .Call(`_rpact_getSimulationMeansLoopCpp`, alternative, kMax, maxNumberOfIterations, designNumber, informationRates, futilityBounds, alpha0Vec, criticalValues, meanRatio, thetaH0, stDev, groups, normalApproximation, plannedSubjects, directionUpper, allocationRatioPlanned, minNumberOfSubjectsPerStage, maxNumberOfSubjectsPerStage, conditionalPower, thetaH1, stDevH1, calcSubjectsFunction)
+}
+
 getSimulationSurvivalCpp <- function(designNumber, kMax, sided, criticalValues, informationRates, conditionalPower, plannedEvents, thetaH1, minNumberOfEventsPerStage, maxNumberOfEventsPerStage, directionUpper, allocation1, allocation2, accrualTime, treatmentGroup, thetaH0, futilityBounds, alpha0Vec, pi1Vec, pi2, eventTime, piecewiseSurvivalTime, cdfValues1, cdfValues2, lambdaVec1, lambdaVec2, phi, maxNumberOfSubjects, maxNumberOfIterations, maxNumberOfRawDatasetsPerStage, kappa) {
     .Call(`_rpact_getSimulationSurvivalCpp`, designNumber, kMax, sided, criticalValues, informationRates, conditionalPower, plannedEvents, thetaH1, minNumberOfEventsPerStage, maxNumberOfEventsPerStage, directionUpper, allocation1, allocation2, accrualTime, treatmentGroup, thetaH0, futilityBounds, alpha0Vec, pi1Vec, pi2, eventTime, piecewiseSurvivalTime, cdfValues1, cdfValues2, lambdaVec1, lambdaVec2, phi, maxNumberOfSubjects, maxNumberOfIterations, maxNumberOfRawDatasetsPerStage, kappa)
 }