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rpact

Confirmatory Adaptive Clinical Trial Design, Simulation, and Analysis.

Functional Range

  • Fixed sample design and designs with interim analysis stages
  • Sample size and power calculation for
    • means (continuous endpoint)
    • rates (binary endpoint)
    • survival trials with flexible recruitment and survival time options
    • count data
  • Simulation tool for means, rates, survival data, and count data
    • Assessment of adaptive sample size/event number recalculations based on conditional power
    • Assessment of treatment selection strategies in multi-arm trials
  • Adaptive analysis of means, rates, and survival data
  • Adaptive designs and analysis for multi-arm trials
  • Adaptive analysis and simulation tools for enrichment design testing means, rates, and hazard ratios
  • Automatic boundary recalculations during the trial for analysis with alpha spending approach, including under- and over-running

Installation

Install the latest CRAN release via

install.packages("rpact")

Development version

To use a feature from the development version, you can install the development version of rpact from GitHub.

# install.packages("pak")
pak::pak("rpact-com/rpact")

Documentation

The documentation is hosted at www.rpact.org

Vignettes

The vignettes are hosted at www.rpact.org/vignettes

The rpact user group

The rpact project has an active user group consisting of decision-makers and users from the pharmaceutical industry and CROs, who meet regularly and, e.g., discuss best practices.

We invite you to be part of the rpact user group: benefit from know-how, shape open source development in Pharma!

Use on corporate computer systems

Please contact us to learn how to use rpact on FDA/GxP-compliant validated corporate computer systems and how to get a copy of the formal validation documentation that is customized and licensed for exclusive use by your company, e.g., to fulfill regulatory requirements. The validation documentation contains the personal access data for performing the installation qualification with testPackage().

www.rpact.com/contact

About

  • rpact is a comprehensive validated[^1] R package for clinical research which
    • enables the design and analysis of confirmatory adaptive group sequential designs
    • is a powerful sample size calculator
    • is a free of charge open-source software licensed under LGPL-3
    • particularly, implements the methods described in the recent monograph by Wassmer and Brannath (2016)

For more information please visit www.rpact.org

  • RPACT is a company which offers
    • enterprise R/Shiny software development services
    • technical support for the rpact package
    • consultancy and user training for scientists using R
    • validated software solutions and R package development for clinical research

For more information please visit www.rpact.com

[^1]: The rpact validation documentation is available exclusively for our customers and supporting members. For more information visit www.rpact.com/services/sla

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Version

Install

install.packages('rpact')

Monthly Downloads

1,194

Version

4.1.0

License

LGPL-3

Issues

Pull Requests

Stars

Forks

Maintainer

Friedrich Pahlke

Last Published

September 27th, 2024

Functions in rpact (4.1.0)

AccrualTime

Accrual Time
AnalysisResults

Basic Class for Analysis Results
AnalysisResultsEnrichmentInverseNormal

Analysis Results Enrichment Inverse Normal
AnalysisResultsMultiArm

Basic Class for Analysis Results Multi-Arm
AnalysisResultsConditionalDunnett

Analysis Results Multi-Arm Conditional Dunnett
AnalysisResultsGroupSequential

Analysis Results Group Sequential
AnalysisResultsFisher

Analysis Results Fisher
AnalysisResultsEnrichmentFisher

Analysis Results Enrichment Fisher
AnalysisResultsInverseNormal

Analysis Results Inverse Normal
AnalysisResultsEnrichment

Basic Class for Analysis Results Enrichment
ConditionalPowerResultsEnrichmentRates

Conditional Power Results Enrichment Rates
AnalysisResultsMultiArmInverseNormal

Analysis Results Multi-Arm Inverse Normal
ConditionalPowerResultsRates

Conditional Power Results Rates
ConditionalPowerResultsSurvival

Conditional Power Results Survival
ConditionalPowerResults

Conditional Power Results
ClosedCombinationTestResults

Analysis Results Closed Combination Test
ConditionalPowerResultsMeans

Conditional Power Results Means
AnalysisResultsMultiHypotheses

Basic Class for Analysis Results Multi-Hypotheses
ConditionalPowerResultsEnrichmentMeans

Conditional Power Results Enrichment Means
AnalysisResultsMultiArmFisher

Analysis Results Multi-Arm Fisher
DatasetRates

Dataset of Rates
NumberOfSubjects

Number Of Subjects
PerformanceScore

Performance Score
DatasetSurvival

Dataset of Survival Data
ParameterSet

Parameter Set
DatasetMeans

Dataset of Means
Dataset

Dataset
PiecewiseSurvivalTime

Piecewise Exponential Survival Time
FieldSet

Field Set
EventProbabilities

Event Probabilities
SimulationResultsEnrichmentMeans

Class for Simulation Results Enrichment Means
SimulationResultsCountData

Class for Simulation Results Count Data
SimulationResultsMultiArmRates

Class for Simulation Results Multi-Arm Rates
PlotSettings

Plot Settings
SimulationResultsEnrichmentRates

Class for Simulation Results Enrichment Rates
PowerAndAverageSampleNumberResult

Power and Average Sample Number Result
SimulationResultsEnrichmentSurvival

Class for Simulation Results Enrichment Survival
SimulationResults

Class for Simulation Results
SimulationResultsMeans

Class for Simulation Results Means
SimulationResultsMultiArmMeans

Class for Simulation Results Multi-Arm Means
StageResultsMeans

Stage Results of Means
SimulationResultsRates

Class for Simulation Results Rates
StageResults

Basic Stage Results
StageResultsEnrichmentMeans

Stage Results Enrichment Means
StageResultsEnrichmentRates

Stage Results Enrichment Rates
SimulationResultsSurvival

Class for Simulation Results Survival
SimulationResultsMultiArmSurvival

Class for Simulation Results Multi-Arm Survival
StageResultsMultiArmMeans

Stage Results Multi Arm Means
StageResultsEnrichmentSurvival

Stage Results Enrichment Survival
StageResultsMultiArmRates

Stage Results Multi Arm Rates
TrialDesignGroupSequential

Group Sequential Design
StageResultsRates

Stage Results of Rates
TrialDesignCharacteristics

Trial Design Characteristics
TrialDesignConditionalDunnett

Conditional Dunnett Design
TrialDesignFisher

Fisher Design
SummaryFactory

Summary Factory
TrialDesignInverseNormal

Inverse Normal Design
StageResultsSurvival

Stage Results of Survival Data
TrialDesign

Basic Trial Design
StageResultsMultiArmSurvival

Stage Results Multi Arm Survival
TrialDesignPlanMeans

Trial Design Plan Means
TrialDesignPlan

Basic Trial Design Plan
TrialDesignPlanCountData

Trial Design Plan Count Data
TrialDesignSet

Class for trial design sets.
TrialDesignPlanSurvival

Trial Design Plan Survival
as.data.frame.PowerAndAverageSampleNumberResult

Coerce Power And Average Sample Number Result to a Data Frame
as.data.frame.AnalysisResults

Coerce AnalysisResults to a Data Frame
as.data.frame.StageResults

Coerce Stage Results to a Data Frame
TrialDesignPlanRates

Trial Design Plan Rates
as.data.frame.ParameterSet

Coerce Parameter Set to a Data Frame
as.data.frame.TrialDesign

Coerce TrialDesign to a Data Frame
dataEnrichmentMeansStratified

Stratified Enrichment Dataset of Means
as251StudentT

Algorithm AS 251: Student T Distribution
as251Normal

Algorithm AS 251: Normal Distribution
as.matrix.FieldSet

Coerce Field Set to a Matrix
as.data.frame.TrialDesignSet

Coerce Trial Design Set to a Data Frame
dataEnrichmentRates

Enrichment Dataset of Rates
as.data.frame.TrialDesignPlan

Coerce Trial Design Plan to a Data Frame
as.data.frame.TrialDesignCharacteristics

Coerce TrialDesignCharacteristics to a Data Frame
dataEnrichmentMeans

Enrichment Dataset of Means
dataEnrichmentSurvivalStratified

Stratified Enrichment Dataset of Survival Data
dataMultiArmRates

Multi-Arm Dataset of Rates
dataMultiArmMeans

Multi-Arm Dataset of Means
dataMeans

One-Arm Dataset of Means
obtain

Extract a single parameter
dataSurvival

One-Arm Dataset of Survival Data
dataRates

One-Arm Dataset of Rates
dataMultiArmSurvival

Multi-Arm Dataset of Survival Data
dataEnrichmentSurvival

Enrichment Dataset of Survival Data
dataEnrichmentRatesStratified

Stratified Enrichment Dataset of Rates
getConditionalPower

Get Conditional Power
getData

Get Simulation Data
plotTypes

Get Available Plot Types
getAnalysisResults

Get Analysis Results
getAccrualTime

Get Accrual Time
getClosedConditionalDunnettTestResults

Get Closed Conditional Dunnett Test Results
getDesignCharacteristics

Get Design Characteristics
getClosedCombinationTestResults

Get Closed Combination Test Results
getDataset

Get Dataset
getConditionalRejectionProbabilities

Get Conditional Rejection Probabilities
getGroupSequentialProbabilities

Get Group Sequential Probabilities
getFinalConfidenceInterval

Get Final Confidence Interval
getDesignGroupSequential

Get Design Group Sequential
getDesignFisher

Get Design Fisher
getLambdaStepFunction

Get Lambda Step Function
getDesignConditionalDunnett

Get Design Conditional Dunnett Test
getDesignSet

Get Design Set
getEventProbabilities

Get Event Probabilities
getDesignInverseNormal

Get Design Inverse Normal
getFinalPValue

Get Final P Value
getObservedInformationRates

Get Observed Information Rates
getNumberOfSubjects

Get Number Of Subjects
rcmd

Get Object R Code
getParameterName

Get Parameter Name
getOutputFormat

Get Output Format
getPerformanceScore

Get Performance Score
getParameterType

Get Parameter Type
getLogLevel

Get Log Level
getParameterCaption

Get Parameter Caption
getLongFormat

Get Long Format
getPowerSurvival

Get Power Survival
getPowerAndAverageSampleNumber

Get Power And Average Sample Number
getPiecewiseSurvivalTime

Get Piecewise Survival Time
getRawData

Get Simulation Raw Data for Survival
getPlotSettings

Get Plot Settings
getPowerRates

Get Power Rates
getRepeatedPValues

Get Repeated P Values
getRepeatedConfidenceIntervals

Get Repeated Confidence Intervals
getPowerMeans

Get Power Means
getPowerCounts

Get Power Counts
getSampleSizeSurvival

Get Sample Size Survival
getSampleSizeMeans

Get Sample Size Means
getSimulationEnrichmentSurvival

Get Simulation Enrichment Survival
getSampleSizeCounts

Get Sample Size Counts
getSampleSizeRates

Get Sample Size Rates
getSimulationMeans

Get Simulation Means
getSimulationEnrichmentRates

Get Simulation Enrichment Rates
getSimulationEnrichmentMeans

Get Simulation Enrichment Means
getSimulationMultiArmMeans

Get Simulation Multi-Arm Means
getSimulationCounts

Get Simulation Counts
kableParameterSet

Create output in Markdown
getSimulationMultiArmSurvival

Get Simulation Multi-Arm Survival
getTestActions

Get Test Actions
getSimulationRates

Get Simulation Rates
getSimulationMultiArmRates

Get Simulation Multi-Arm Rates
getSimulationSurvival

Get Simulation Survival
getStageResults

Get Stage Results
getWideFormat

Get Wide Format
knit_print.FieldSet

Print Field Set in Markdown Code Chunks
knit_print.ParameterSet

Print Parameter Set in Markdown Code Chunks
knit_print.SummaryFactory

Print Summary Factory in Markdown Code Chunks
names.StageResults

Names of a Stage Results Object
mvstud

Original Algorithm AS 251: Student T Distribution
mvnprd

Original Algorithm AS 251: Normal Distribution
names.AnalysisResults

Names of a Analysis Results Object
param_accrualIntensity

Parameter Description: Accrual Intensity
length.TrialDesignSet

Length of Trial Design Set
names.FieldSet

Names of a Field Set Object
names.TrialDesignSet

Names of a Trial Design Set Object
names.SimulationResults

Names of a Simulation Results Object
param_alpha

Parameter Description: Alpha
param_activeArms

Parameter Description: Active Arms
param_alternative

Parameter Description: Alternative
param_accrualTime

Parameter Description: Accrual Time
param_accrualIntensity_counts

Parameter Description: accrualIntensity for Counts
param_allocationRatioPlanned_sampleSize

Parameter Description: Allocation Ratio Planned With Optimum Option
param_adaptations

Parameter Description: Adaptations
param_accrualTime_counts

Parameter Description: accrualTime for Counts
param_accrualIntensityType

Parameter Description: Accrual Intensity Type
param_allocationRatioPlanned

Parameter Description: Allocation Ratio Planned
param_conditionalPowerSimulation

Parameter Description: Conditional Power
param_bindingFutility

Parameter Description: Binding Futility
param_dataInput

Parameter Description: Data Input
param_design

Parameter Description: Design
param_alternative_simulation

Parameter Description: Alternative for Simulation
param_calcSubjectsFunction

Parameter Description: Calculate Subjects Function
param_calcEventsFunction

Parameter Description: Calculate Events Function
param_beta

Parameter Description: Beta
param_design_with_default

Parameter Description: Design with Default
param_directionUpper

Parameter Description: Direction Upper
param_digits

Parameter Description: Digits
param_conditionalPower

Parameter Description: Conditional Power
param_dropoutRate2

Parameter Description: Dropout Rate (2)
param_dropoutRate1

Parameter Description: Dropout Rate (1)
param_effectList

Parameter Description: Effect List
param_informationRates

Parameter Description: Information Rates
param_epsilonValue

Parameter Description: Epsilon Value
param_eventTime

Parameter Description: Event Time
param_includeAllParameters

Parameter Description: Include All Parameters
param_informationEpsilon

Parameter Description: Information Epsilon
param_intersectionTest_Enrichment

Parameter Description: Intersection Test
param_lambda_counts

Parameter Description: lambda for Counts
param_dropoutTime

Parameter Description: Dropout Time
param_lambda2

Parameter Description: Lambda (2)
param_effectMeasure

Parameter Description: Effect Measure
param_nMax

Parameter Description: N_max
param_hazardRatio

Parameter Description: Hazard Ratio
param_lambda1

Parameter Description: Lambda (1)
param_fixedExposureTime_counts

Parameter Description: fixedExposureTime for Counts
param_minNumberOfSubjectsPerStage

Parameter Description: Minimum Number Of Subjects Per Stage
param_groups

Parameter Description: Number Of Treatment Groups
param_effectMatrix

Parameter Description: Effect Matrix
param_lambda1_counts

Parameter Description: lambda (1) for Counts
param_maxNumberOfSubjectsPerStage

Parameter Description: Maximum Number Of Subjects Per Stage
param_pi2_survival

Parameter Description: Pi (2) for Survival Data
param_lambda2_counts

Parameter Description: lambda (2) for Counts
param_maxNumberOfEventsPerStage

Parameter Description: Max Number Of Events Per Stage
param_kappa

Parameter Description: Kappa
param_maxNumberOfSubjects

Parameter Description: Maximum Number Of Subjects
param_followUpTime_counts

Parameter Description: followUpTime for Counts
param_gED50

Parameter Description: G ED50
param_grid

Parameter Description: Grid (Output Specification Of Multiple Plots)
param_pi1_rates

Parameter Description: Pi (1) for Rates
param_selectPopulationsFunction

Parameter Description: Select Populations Function
param_intersectionTest_MultiArm

Parameter Description: Intersection Test
param_palette

Parameter Description: Palette
param_selectArmsFunction

Parameter Description: Select Arms Function
param_plannedSubjects

Parameter Description: Planned Subjects
param_plannedCalendarTime

Parameter Description: Planned Calendar Time
param_nPlanned

Parameter Description: N Planned
param_rValue

Parameter Description: R Value
param_seed

Parameter Description: Seed
param_piecewiseSurvivalTime

Parameter Description: Piecewise Survival Time
param_plannedEvents

Parameter Description: Planned Events
param_maxNumberOfIterations

Parameter Description: Maximum Number Of Iterations
param_stage

Parameter Description: Stage
param_sided

Parameter Description: Sided
param_slope

Parameter Description: Slope
param_stDevSimulation

Parameter Description: Standard Deviation for Simulation
param_theta

Parameter Description: Theta
param_tolerance

Parameter Description: Tolerance
param_typeOfComputation

Parameter Description: Type Of Computation
param_successCriterion

Parameter Description: Success Criterion
param_niceColumnNamesEnabled

Parameter Description: Nice Column Names Enabled
param_showStatistics

Parameter Description: Show Statistics
param_showSource

Parameter Description: Show Source
param_maxInformation

Parameter Description: Maximum Information
param_legendPosition

Parameter Description: Legend Position On Plots
param_median2

Parameter Description: Median (2)
param_stDevH1

Parameter Description: Standard Deviation Under Alternative
param_thetaH0

Parameter Description: Theta H0
param_stDev

Parameter Description: Standard Deviation
param_minNumberOfEventsPerStage

Parameter Description: Min Number Of Events Per Stage
param_thetaH1

Parameter Description: Effect Under Alternative
param_normalApproximation

Parameter Description: Normal Approximation
param_kMax

Parameter Description: Maximum Number of Stages
plot.AnalysisResults

Analysis Results Plotting
param_overdispersion_counts

Parameter Description: overdispersion for Counts
plot.EventProbabilities

Event Probabilities Plotting
param_varianceOption

Parameter Description: Variance Option
plot.Dataset

Dataset Plotting
param_typeOfDesign

Parameter Description: Type of Design
param_maxNumberOfSubjects_survival

Parameter Description: Maximum Number Of Subjects For Survival Endpoint
param_typeOfSelection

Parameter Description: Type of Selection
param_pi1_survival

Parameter Description: Pi (1) for Survival Data
param_stratifiedAnalysis

Parameter Description: Stratified Analysis
param_pi2_rates

Parameter Description: Pi (2) for Rates
param_typeOfShape

Parameter Description: Type Of Shape
param_populations

Parameter Description: Populations
param_plotSettings

Parameter Description: Plot Settings
param_median1

Parameter Description: Median (1)
param_stageResults

Parameter Description: Stage Results
param_theta_counts

Parameter Description: theta for Counts
param_three_dots

Parameter Description: "..."
plot.TrialDesign

Trial Design Plotting
plot.SimulationResults

Simulation Results Plotting
plot.SummaryFactory

Summary Factory Plotting
plot.TrialDesignPlan

Trial Design Plan Plotting
plot.ParameterSet

Parameter Set Plotting
param_threshold

Parameter Description: Threshold
param_plotPointsEnabled

Parameter Description: Plot Points Enabled
param_three_dots_plot

Parameter Description: "..." (optional plot arguments)
plot.TrialDesignSet

Trial Design Set Plotting
plot.NumberOfSubjects

Number Of Subjects Plotting
plot.TrialDesignSummaries

Plot Trial Design Summaries
print.Dataset

Print Dataset Values
rpact

rpact - Confirmatory Adaptive Clinical Trial Design and Analysis
print.TrialDesignCharacteristics

Trial Design Characteristics Printing
print.ParameterSet

Print Parameter Set Values
print.FieldSet

Print Field Set Values
print.SimulationResults

Print Simulation Results
print.TrialDesignSummaries

Print Trial Design Summaries
param_userAlphaSpending

Parameter Description: User Alpha Spending
plot.StageResults

Stage Results Plotting
print.SummaryFactory

Summary Factory Printing
rawDataTwoArmNormal

Raw Dataset Of A Two Arm Continuous Outcome With Covariates
resetLogLevel

Reset Log Level
printCitation

Print Citation
readDataset

Read Dataset
setOutputFormat

Set Output Format
summary.TrialDesignSet

Trial Design Set Summary
summary.ParameterSet

Parameter Set Summary
setLogLevel

Set Log Level
utilitiesForSurvivalTrials

Survival Helper Functions for Conversion of Pi, Lambda, Median
utilitiesForPiecewiseExponentialDistribution

The Piecewise Exponential Distribution
readDatasets

Read Multiple Datasets
writeDatasets

Write Multiple Datasets
summary.Dataset

Dataset Summary
summary.AnalysisResults

Analysis Results Summary
writeDataset

Write Dataset
testPackage

Test Package
test_plan_section

Test Plan Section