rpact 3.3.0

New features

• Two-sided beta-spending approach with binding and non-binding futility bounds
• Delayed response utility added in design specification

Improvements, issues, and changes

• getSimulationMultiArmSurvival(): single stage treatment arm specific event numbers account for selection procedure
• User defined selection function can be used in getSimulationEnrichmentRates() and getSimulationEnrichmentSurvival()
• Design summary extended by information of getDesignCharacteristics()
• getSimulationSurvival(): the result object now contains the new parameter overallEventsPerStage; the name of eventsPerStage in the print output has been corrected (was “cumulative” by mistake)
• getSimulationSurvival(): the result object now contains the new parameter overallEventsPerStage, which contains the values previously given in eventsPerStage (it was “cumulative” by mistake); eventsPerStage contains now the non-cumulative values as expected
• Minor improvements

rpact 3.2.3

• Performance of group sequential and Fisher’s combination test designs improved
• ‘register’ storage class specifier removed from C++ sources
• Minor improvements

rpact 3.2.2

• Performance of group sequential and Fisher’s combination test designs improved (by translating from R to C++)
• Numerical issue in analysis time calculation for survival design in specific cases resolved
• The internally used minimum quantile function value was changed from stats::qnorm(1e-323) to stats::qnorm(1e-100)
• Unit tests extended
• Minor improvements

rpact 3.2.1

• C++ warning “using integer absolute value function ‘abs’ when argument is of floating point type” under r-devel-linux-x86_64-debian-clang removed
• getDataset: support of emmeans result objects as input improved
• getAnalysisResults(): issue with zero values in the argument ‘userAlphaSpending’ fixed
• Minor improvements

rpact 3.2.0

New features

• Simulation tools for enrichment design testing means, rates, and hazard ratios: function getSimulationEnrichmentMeans(), getSimulationEnrichmentRates(), getSimulationEnrichmentSimulation() available for simulation of enrichment designs; note that this is a novel implementation, hence experimental
• getDesignGroupSequential() / getDesignInverseNormal(): new typeOfDesign = “noEarlyEfficacy” added

Improvements, issues, and changes

• getSimulationSurvival(): bug fixed for accruallIntensity = 0 at some accrual intervals
• For observed conditional power, standardized theta not truncated to 0 any more in getSimulationMultiArmMeans(), getSimulationMultiArmRates(), and getSimulationMultiArmSurvival()
• Conditional power calculation for analysis rates takes into account differently the null value of condErrorRate
• Function testPackage(): a problem with downloading full set of unit tests under Debian/Linux has been fixed
• Generic function kable() improved: optional knitr::kable arguments enabled, e.g., format
• In print and summary output, “overall” renamed to “cumulative” if means, stDevs, or rate are calculated over stages rather than stage-wise
• getDataset: support of emmeans result objects as input improved
• Numerical accuracy of qnorm() calculations improved
• Analysis enrichment results now support the generic function as.data.frame()
• Naming of the stage results parameters in the print output improved
• New example data added: “rawDataTwoArmNormal”
• Issue in summary fixed: earlyStop and rejectPerStage were no longer displayed
• Minor improvements

rpact 3.1.1

• Performance of two-sided Pampallona & Tsiatis design improved
• 12 example datasets added
• Sample sizes in plots now have the same format as in print output; format can be changed using setOutputFormat()
• getDataset supports emmeans result objects as input
• Print output of simulation results improved
• Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R
• Plot label interface for configuration via the rpact Shiny app implemented
• Minor improvements

rpact 3.1.0

New features

• Analysis tools for enrichment design testing means, rates, and hazard ratios: function getAnalysisResults() generalized for enrichment designs; function getDataset() generalized for entering stratified data; manual extended for enrichment designs
• Automatic boundary recalculations during the trial for analysis with alpha spending approach, including under- and over-running: setup via the optional parameters ‘maxInformation’ and ‘informationEpsilon’ in function getAnalysisResults()
• The new function getObjectRCode() (short: rcmd()) returns the original R command which produced any rpact result object, including all dependencies
• getWideFormat() and getLongFormat() return a dataset object in wide format (unstacked) or long format (narrow, stacked)
• Generic function kable() returns the output of an rpact result object formatted in Markdown.
• Generic function t() returns the transpose of an rpact result object

Improvements, issues, and changes

• New argument ‘plotSettings’ added to all plot functions
• Summary for design, simulation, and analysis unified and extended
• Issue in getDesignFisher() fixed: getDesignFisher(method = "noInteraction", kMax = 3) and getDesignFisher(method = "noInteraction") produced different results
• ‘normalApproximation’ default value changed to TRUE for multi-arm analysis of rates
• Repeated p-values: in search algorithm, upper bound of significance level corrected when considering binding futility bounds
• testPackage(): the default call is now running only a small subset of all available unit tests; with the new argument ‘connection’ the owners of the rpact validation documentation can enter a ‘token’ and a ‘secret’ to get full access to all unit tests
• Scaling of grid plots improved
• Minor improvements

rpact 3.0.4

• Beta-spending function approach with binding futility bounds
• Pampallona & Tsiatis design with binding and non-binding futility bounds
• Argument ‘accrualIntensityType’ added to getSampleSizeSurvival(), getSimulationSurvival(), getNumberOfSubjects(), and getEventProbabilities()
• Specification of Weibull survival times possible through definition of hazard rates or medians in simulation tool
• Minor improvements

rpact 3.0.3

• New utility functions getParameterCaption() and getParameterName() implemented
• Design parameters added to simulation print output
• Generic function as.matrix() improved for several result objects
• Issue in getAvailablePlotTypes() for sample size and power results fixed
• Issue for getDesignFisher(kMax = 1) in getSimulationMultiArm...() fixed
• getSimulationMultiArmSurvival(): correlation of log-rank statistics revised and improved
• getSimulationMultiArmMeans(): name of the first effectMeasure option “effectDifference” changed to “effectEstimate”
• getSimulation[MultiArm][Means/Rates/Survival](): argument ‘showStatistics’ now works correctly and is consistently FALSE by default for multi-arm and non-multi-arm
• getSimulation[MultiArm]Survival(): generic function summary() improved
• getAnalysisResults(): generic function summary() improved
• getAccrualTime(): improved and new argument ‘accrualIntensityType’ added
• Header text added to design summaries
• getSampleSizeSurvival(): field ‘studyDurationH1’ in result object was replaced by ‘studyDuration’, i.e., ‘studyDurationH1’ is deprecated and will be removed in future versions
• Minor changes in the inline help and manual
• Minor improvements

rpact 3.0.2

• getSimulationMultiArmSurvival(): plannedEvents redefined as overall events over treatment arms
• getStageResults(): element overallPooledStDevs added; print output improved
• Unit tests improved: test coverage and references to the functional specification optimized
• plot type 13 of getSampleSizeSurvival() with user defined lambdas with different lengths: issue fixed
• Minor improvements

rpact 3.0.1

• Vignette “rpact: Getting Started” included into the package
• New summary output option “rpact.summary.width” added
• Generic function summary() improved for several result objects
• Result output of function testPackage() improved
• getSimulationMultiArm[Means/Rates/Survival](): stage index corrected for user defined calcSubjectsFunction or calcEventsFunction
• getSimulationMultiArmRates(): adjustment for identical simulated rates to account for ties
• getSimulationMultiArmSurvival(): corrected correlation of test statistics
• Output formatting improved
• Minor improvements

rpact 3.0.0

New features

• Simulation tools for multi-arm design testing means, rates, and hazard ratios
• Analysis tools for multi-arm design testing means, rates, and hazard ratios
• getSimulationRates(): exact versions for testing a rate (one-sample case) and equality of rates (two-sample case)
• getDataset: multi-arm datasets for means, rates, and survival data
• Analysis of fixed designs
• Summary for analysis and simulation result objects newly implemented
• Summary for most rpact result objects substantially improved and enhanced
• getEventProbabilities(): plot of result object
• getNumberOfSubjects(): plot of result object
• Visual comparison of two designs: plot(design1, design2)
• Functions setOutputFormat and getOutputFormat implemented: definition of user defined output formats
• getSimulationMeans(): thetaH1 and stDevH1 can be specified for assessment of sample size recalculation (replaces thetaStandardized)
• getSimulationSurvival(): separate p-values added to the aggregated simulation data for Fisher designs
• getSimulationMeans(), getSimulationRates(): Cumulated number of subjects integrated in getData object
• getSimulation[MultiArm][Means/Rates/Survival](): new logical argument ‘showStatistics’ added
• Example datasets (csv files) added to the package
• plot type “all”: plot all available plots of an object in one step using plot(x, type = "all")
• plot type improved: ‘type’ now can be a vector, e.g., plot(x, type = c(1, 3))
• plot(x, grid = 1): new plot argument ‘grid’ enables the plotting of 2 or more plots in one graphic

Improvements, issues, and changes

• getAnalysisResults(): list output implemented analogous to the output of all other rpact objects
• getAnalysisResults(): the following stage result arguments were removed from result object because they were redundant: effectSizes, testStatistics, and pValues. Please use the ‘.stageResults’ object to access them, e.g., results$.stageResults$effectSizes
• getAnalysisResults(): the following design arguments were removed from result object because they were redundant: stages, informationRates, criticalValues, futilityBounds, alphaSpent, and stageLevels. Please use the ‘.design’ object to access them, e.g., results$.design$informationRates
• Optional argument ‘stage’ removed from functions getConditionalPower, getConditionalRejectionProbabilities, getFinalPValue, getRepeatedPValues, and getTestActions
• Function testPackage improved, e.g., results will be displayed now on screen
• Help system renewed and approved, e.g., help for corresponding generic functions (e.g., plot) linked where applicable
• Function getPiecewiseSurvivalTime improved: pi1 and pi2 will not be calculated any longer for lambda- or median-based definitions; eventTime only required for pi-based definitions
• plot(x, showSource = TRUE) improved for all rpact result objects x
• Performance of plotting analysis results of Fisher designs improved
• getSimulationRates(): issue for futility stopping for Fisher’s combination test fixed
• getSimulationSurvival(): issue for expected number of events fixed
• getSimulationSurvival(): if eventsNotAchieved > 0, rejection/futility rate and analysis time is estimated for valid simulation runs
• getSimulationSurvival(): output improved for lambda1/median1/hazardRatio with length > 1
• getSampleSizeSurvival(): calculation of the maximum number of subjects given the provided argument ‘followUpTime’ improved
• getPiecewiseSurvivalTime(): delayed response via list-based piecewiseSurvivalTime definition enabled
• getAccrualTime() / getSimulationSurvival(): issue with the calculation of absolute accrual intensity by given relative accrual intensity fixed
• getRawData(): issue for multiple pi1 solved
• Implementation of the generic function ‘names’ improved
• Test coverage improved: lots of new unit tests added
• License information in the DESCRIPTION file corrected: changed from GPL-3 to LGPL-3
• Minor improvements

rpact 2.0.6

• Boundaries on effect scale for testing means now accounts for the unknown variance case
• getAnalysisSurvival(): calculation of stage wise results not more in getStageResults
• getStageResults(): the calculation of ‘effectSizes’ for survival data and thetaH0 != 1 was corrected
• getDataset() of survival data: issue with the internal storage of log ranks fixed
• Sample size plot: issue for kMax = 1 fixed
• getSampleSizeSurvival() with piecewise survival time: issue with calculation of ‘maxNumberOfSubjects’ for given ‘followUpTime’ fixed
• Internal Shiny app interface improved
• Minor improvements

rpact 2.0.5

• Assumed median survival time: get[SampleSize/Power/Simulation]Survival now support direct input of arguments ‘median1’ and ‘median2’
• Output of generic function summary() improved
• Plot type 5 of getPower[…] and getSimulation[…] objects improved
• Output of getSampleSizeSurvival() with given maxNumberOfSubjects improved
• Output of get[SampleSize/Power]Survival() for Kappa != 1 improved
• Assert function for minNumberOfSubjectsPerStage corrected for undefined conditionalPower
• Two-sided boundaries on effect scale in survival design improved
• Error in summary() for getDesign[...]() fixed
• Other minor improvements

rpact 2.0.4

• Incorrect output of function summary() fixed for getSampleSize[...]() and getPower[...]()
• as.data.frame: default value of argument ‘niceColumnNamesEnabled’ changed from TRUE to FALSE

rpact 2.0.3

New features

• Plot function for Fisher design implemented
• Generic function summary() implemented for getDesign[...](), getSampleSize[...](), getPower[...](), and getSimulation[...]() results: a simple boundary summary will be displayed

Improvements, issues, and changes

• Generic function as.data.frame improved for getDesign[...](), getSampleSize[...](), getPower[...](), and getSimulation[...]() results
• Output of getStageResults() improved
• Improvements for Shiny app compatibility and better Shiny app performance
• Repeated p-values are no longer calculated for typeOfDesign = “WToptimum”
• Piecewise survival time improved for numeric definition: median and pi will not be calculated and displayed any longer
• Plot: legend title and tick mark positioning improved; optional arguments xlim and ylim implemented
• Sample size/power: usage of argument ‘twoSidedPower’ optimized
• Performance of function rpwexp/getPiecewiseExponentialRandomNumbers improved (special thanks to Marcel Wolbers for his example code)
• For group sequential designs a warning will be displayed if information rates from design not according to data information
• Format for output of standard deviation optimized

rpact 2.0.2

• Minor corrections in the inline help
• Labeling of lower and upper critical values (effect scale) reverted
• Simulation for Fisher’s combination test corrected
• Parameter minNumberOfAdditionalEventsPerStage renamed to minNumberOfEventsPerStage
• Parameter maxNumberOfAdditionalEventsPerStage renamed to maxNumberOfEventsPerStage
• Parameter minNumberOfAdditionalSubjectsPerStage renamed to minNumberOfSubjectsPerStage
• Parameter maxNumberOfAdditionalSubjectsPerStage renamed to maxNumberOfSubjectsPerStage
• Output of function getAccrualTime() improved
• Validation of arguments maxNumberOfIterations, allocation1, and allocation2 added: check for positive integer
• Function getSampleSizeSurvival() improved: numeric search for accrualTime if followUpTime is given
• Default value improved for analysis tools: if no effect was specified for conditional power calculation, the observed effect is selected
• Fixed: function getDataset produced an error if only one log-rank value and one event was defined
• Number of subjects per treatment arm are provided in output of simulation survival if allocation ratio != 1
• Function getSimulationSurvival improved: first value of minNumberOfEventsPerStage and maxNumberOfEventsPerStage must be NA or equal to first value of plannedSubjects

rpact 2.0.1

• Function base::isFALSE replaced to guarantee R 3.4.x compatibility
• C++ compiler warning on r-devel-linux-x86_64-debian-clang system removed
• C++ compiler error on r-patched-solaris-x86 system fixed

rpact 2.0.0

New features

• Power calculation at given or adapted sample size for means, rates and survival data
• Sample size and power calculation for survival trials with piecewise accrual time and intensity
• Sample size and power calculation for survival trials with exponential survival time, piecewise exponential survival time and survival times that follow a Weibull distribution
• Simulation tool for survival trials; our simulator is very fast because it was implemented with C++. Adaptive event number recalculations based on conditional power can be assessed
• Simulation tool for designs with continuous and binary endpoints. Adaptive sample size recalculations based on conditional power can be assessed
• Comprehensive and unified tool for performing sample size calculation for fixed sample size design
• Enhanced plot functionalities

Improvements, issues, and changes

• Fisher design, analysis of means or rates, conditional rejection probabilities (CRP): calculation issue fixed for stage > 2
• Call of getSampleSize[Means/Rates/Survival] without design argument implemented
• For all set.seed() calls ‘kind’ and ‘normal.kind’ were specified as follows: kind = “Mersenne-Twister”, normal.kind = “Inversion”
• Minor code optimizations, e.g. ‘return()’ replaced by ‘return(invisible())’ if reasonable
• Bug in readDatasets() fixed: variable names ‘group’ and ‘groups’ are now accepted
• “Overall reject per stage” and “Overall futility per stage” renamed to “Overall reject” and “Overall futility”, respectively (also variable names)
• Labels “events..” and “..patients..” consistently changed to “# events..” and “# patients…”, respectively
• Output format for ‘allocationRatioPlanned’ specified
• Method ‘show’ of class ‘ParameterSet’ expanded: R Markdown output features implemented
• getSampleSizeSurvival(): argument ‘maxNumberOfPatients’ was renamed in ‘maxNumberOfSubjects’
• Result output, inline help and documentation: the word ‘patient’ was replaced by ‘subject’
• Variables ‘numberOfSubjectsGroup1’ and ‘numberOfSubjectsGroup2’ were renamed to ‘numberOfSubjects1’ and ‘numberOfSubjects1’
• Final p-values for two-sided test (group sequential, inverse normal, and Fisher combination test) available
• Upper and lower boundaries on effect scale for testing rates in two samples

rpact 1.0.0

• First release of rpact