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rpact

Confirmatory Adaptive Clinical Trial Design, Simulation, and Analysis.

Functional Range

  • Sample size and power calculation for
    • means (continuous endpoint)
    • rates (binary endpoint)
    • survival trials with
      • piecewise accrual time and intensity
      • piecewise exponential survival time
      • survival times that follow a Weibull distribution
  • Fixed sample design and designs with interim analysis stages
  • Simulation tool for means, rates, and survival 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")

Documentation

The documentation is hosted at https://www.rpact.org

Vignettes

The vignettes are hosted at https://www.rpact.com/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

3.3.4

License

LGPL-3

Issues

Pull Requests

Stars

Forks

Maintainer

Friedrich Pahlke

Last Published

February 14th, 2023

Functions in rpact (3.3.4)

AnalysisResults

Basic Class for Analysis Results
AccrualTime

Accrual Time
AnalysisResultsMultiArmFisher

Analysis Results Multi-Arm Fisher
AnalysisResultsEnrichmentInverseNormal

Analysis Results Enrichment Inverse Normal
AnalysisResultsConditionalDunnett

Analysis Results Multi-Arm Conditional Dunnett
AnalysisResultsInverseNormal

Analysis Results Inverse Normal
AnalysisResultsMultiArm

Basic Class for Analysis Results Multi-Arm
AnalysisResultsEnrichment

Basic Class for Analysis Results Enrichment
AnalysisResultsFisher

Analysis Results Fisher
SimulationResultsEnrichmentMeans

Class for Simulation Results Enrichment Means
ConditionalPowerResults

Conditional Power Results
ParameterSet

Parameter Set
ClosedCombinationTestResults

Analysis Results Closed Combination Test
NumberOfSubjects

Number Of Subjects
DatasetRates

Dataset of Rates
PiecewiseSurvivalTime

Piecewise Exponential Survival Time
DatasetSurvival

Dataset of Survival Data
Dataset

Dataset
DatasetMeans

Dataset of Means
StageResultsMeans

Stage Results of Means
StageResultsRates

Stage Results of Rates
FieldSet

Field Set
EventProbabilities

Event Probabilities
SummaryFactory

Summary Factory
StageResultsSurvival

Stage Results of Survival Data
SimulationResultsEnrichmentRates

Class for Simulation Results Enrichment Rates
SimulationResultsMultiArmMeans

Class for Simulation Results Multi-Arm Means
PlotSettings

Plot Settings
SimulationResultsMultiArmRates

Class for Simulation Results Multi-Arm Rates
TrialDesignGroupSequential

Group Sequential Design
TrialDesignInverseNormal

Inverse Normal Design
TrialDesignConditionalDunnett

Conditional Dunnett Design
TrialDesignFisher

Fisher Design
TrialDesignSet

Class for trial design sets.
SimulationResults

Class for Simulation Results
PowerAndAverageSampleNumberResult

Power and Average Sample Number Result
as.data.frame.AnalysisResults

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

Coerce Parameter Set to a Data Frame
SimulationResultsMultiArmSurvival

Class for Simulation Results Multi-Arm Survival
as.data.frame.TrialDesignSet

Coerce Trial Design Set to a Data Frame
TrialDesignCharacteristics

Trial Design Characteristics
TrialDesignPlanRates

Trial Design Plan Rates
SimulationResultsRates

Class for Simulation Results Rates
TrialDesign

Basic Trial Design
TrialDesignPlanSurvival

Trial Design Plan Survival
dataEnrichmentRates

Enrichment Dataset of Rates
as.data.frame.StageResults

Coerce Stage Results to a Data Frame
as.data.frame.PowerAndAverageSampleNumberResult

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

Coerce TrialDesignCharacteristics to a Data Frame
dataEnrichmentRatesStratified

Stratified Enrichment Dataset of Rates
as.data.frame.TrialDesign

Coerce TrialDesign to a Data Frame
dataEnrichmentSurvival

Enrichment Dataset of Survival Data
as.matrix.FieldSet

Coerce Field Set to a Matrix
AnalysisResultsMultiHypotheses

Basic Class for Analysis Results Multi-Hypotheses
SimulationResultsMeans

Class for Simulation Results Means
dataMultiArmSurvival

Multi-Arm Dataset of Survival Data
AnalysisResultsMultiArmInverseNormal

Analysis Results Multi-Arm Inverse Normal
dataMultiArmRates

Multi-Arm Dataset of Rates
getData

Get Simulation Data
SimulationResultsEnrichmentSurvival

Class for Simulation Results Enrichment Survival
getConditionalRejectionProbabilities

Get Conditional Rejection Probabilities
as.data.frame.TrialDesignPlan

Coerce Trial Design Plan to a Data Frame
SimulationResultsSurvival

Class for Simulation Results Survival
getClosedConditionalDunnettTestResults

Get Closed Conditional Dunnett Test Results
getConditionalPower

Get Conditional Power
StageResults

Basic Stage Results
dataEnrichmentMeans

Enrichment Dataset of Means
dataEnrichmentMeansStratified

Stratified Enrichment Dataset of Means
getAccrualTime

Get Accrual Time
TrialDesignPlanMeans

Trial Design Plan Means
TrialDesignPlan

Basic Trial Design Plan
getAnalysisResults

Get Analysis Results
getFinalConfidenceInterval

Get Final Confidence Interval
getFinalPValue

Get Final P Value
getDesignCharacteristics

Get Design Characteristics
getDataset

Get Dataset
dataSurvival

One-Arm Dataset of Survival Data
dataRates

One-Arm Dataset of Rates
getDesignInverseNormal

Get Design Inverse Normal
dataMeans

One-Arm Dataset of Means
getDesignGroupSequential

Get Design Group Sequential
getNumberOfSubjects

Get Number Of Subjects
plotTypes

Get Available Plot Types
getDesignConditionalDunnett

Get Design Conditional Dunnett Test
getDesignFisher

Get Design Fisher
getLogLevel

Get Log Level
getParameterName

Get Parameter Name
getParameterCaption

Get Parameter Caption
dataEnrichmentSurvivalStratified

Stratified Enrichment Dataset of Survival Data
dataMultiArmMeans

Multi-Arm Dataset of Means
getRawData

Get Simulation Raw Data for Survival
getPowerSurvival

Get Power Survival
getGroupSequentialProbabilities

Get Group Sequential Probabilities
getLambdaStepFunction

Get Lambda Step Function
getPowerMeans

Get Power Means
getPlotSettings

Get Plot Settings
getLongFormat

Get Long Format
getClosedCombinationTestResults

Get Closed Combination Test Results
rcmd

Get Object R Code
getPowerRates

Get Power Rates
getDesignSet

Get Design Set
getEventProbabilities

Get Event Probabilities
getObservedInformationRates

Get Observed Information Rates
getRepeatedConfidenceIntervals

Get Repeated Confidence Intervals
getRepeatedPValues

Get Repeated P Values
getPowerAndAverageSampleNumber

Get Power And Average Sample Number
getPiecewiseSurvivalTime

Get Piecewise Survival Time
getOutputFormat

Get Output Format
getPerformanceScore

Get Performance Score
getSimulationMultiArmRates

Get Simulation Multi-Arm Rates
getSimulatedRejectionsDelayedResponse

Simulates the rejection probability of a delayed response group sequential design with specified parameters. By default, delta = 0, i.e., the Type error rate is simulated.
getSampleSizeRates

Get Sample Size Rates
getSimulationEnrichmentRates

Get Simulation Enrichment Rates
getSimulationEnrichmentMeans

Get Simulation Enrichment Means
getSampleSizeSurvival

Get Sample Size Survival
getSimulationMeans

Get Simulation Means
getSimulationEnrichmentSurvival

Get Simulation Enrichment Survival
getSampleSizeMeans

Get Sample Size Means
getSimulationMultiArmMeans

Get Simulation Multi-Arm Means
getTestActions

Get Test Actions
getSimulationRates

Get Simulation Rates
length.TrialDesignSet

Length of Trial Design Set
getSimulationSurvival

Get Simulation Survival
kable.ParameterSet

Create output in Markdown
getWideFormat

Get Wide Format
getSimulationMultiArmSurvival

Get Simulation Multi-Arm Survival
getStageResults

Get Stage Results
param_accrualIntensity

Parameter Description: Accrual Intensity
names.AnalysisResults

Names of a Analysis Results Object
param_adaptations

Parameter Description: Adaptations
param_allocationRatioPlanned

Parameter Description: Allocation Ratio Planned
names.SimulationResults

Names of a Simulation Results Object
names.FieldSet

Names of a Field Set Object
names.StageResults

Names of a Stage Results Object
param_calcEventsFunction

Parameter Description: Calculate Events Function
kable

Create tables in Markdown
param_conditionalPower

Parameter Description: Conditional Power
param_calcSubjectsFunction

Parameter Description: Calculate Subjects Function
param_accrualIntensityType

Parameter Description: Accrual Intensity Type
param_conditionalPowerSimulation

Parameter Description: Conditional Power
param_digits

Parameter Description: Digits
param_design_with_default

Parameter Description: Design with Default
param_bindingFutility

Parameter Description: Binding Futility
param_accrualTime

Parameter Description: Accrual Time
param_effectMatrix

Parameter Description: Effect Matrix
param_beta

Parameter Description: Beta
param_epsilonValue

Parameter Description: Epsilon Value
param_activeArms

Parameter Description: Active Arms
param_directionUpper

Parameter Description: Direction Upper
param_dropoutRate1

Parameter Description: Dropout Rate (1)
param_effectMeasure

Parameter Description: Effect Measure
param_effectList

Parameter Description: Effect List
names.TrialDesignSet

Names of a Trial Design Set Object
param_informationEpsilon

Parameter Description: Information Epsilon
param_lambda2

Parameter Description: Lambda (2)
param_lambda1

Parameter Description: Lambda (1)
param_informationRates

Parameter Description: Information Rates
param_alternative

Parameter Description: Alternative
param_alternative_simulation

Parameter Description: Alternative for Simulation
param_median1

Parameter Description: Median (1)
param_maxNumberOfSubjects_survival

Parameter Description: Maximum Number Of Subjects For Survival Endpoint
param_allocationRatioPlanned_sampleSize

Parameter Description: Allocation Ratio Planned With Optimum Option
param_alpha

Parameter Description: Alpha
param_design

Parameter Description: Design
param_maxNumberOfSubjects

Parameter Description: Maximum Number Of Subjects
param_maxNumberOfSubjectsPerStage

Parameter Description: Maximum Number Of Subjects Per Stage
param_groups

Parameter Description: Number Of Treatment Groups
param_dataInput

Parameter Description: Data Input
param_maxInformation

Parameter Description: Maximum Information
param_legendPosition

Parameter Description: Legend Position On Plots
param_grid

Parameter Description: Grid (Output Specification Of Multiple Plots)
param_pi2_rates

Parameter Description: Pi (2) for Rates
param_pi2_survival

Parameter Description: Pi (2) for Survival Data
param_nPlanned

Parameter Description: N Planned
param_niceColumnNamesEnabled

Parameter Description: Nice Column Names Enabled
param_pi1_survival

Parameter Description: Pi (1) for Survival Data
param_pi1_rates

Parameter Description: Pi (1) for Rates
param_intersectionTest_MultiArm

Parameter Description: Intersection Test
param_intersectionTest_Enrichment

Parameter Description: Intersection Test
param_stage

Parameter Description: Stage
param_populations

Parameter Description: Populations
param_plotSettings

Parameter Description: Plot Settings
param_stDevSimulation

Parameter Description: Standard Deviation for Simulation
param_selectArmsFunction

Parameter Description: Select Arms Function
param_selectPopulationsFunction

Parameter Description: Select Populations Function
param_maxNumberOfEventsPerStage

Parameter Description: Max Number Of Events Per Stage
param_thetaH1

Parameter Description: Effect Under Alternative
param_gED50

Parameter Description: G ED50
param_dropoutRate2

Parameter Description: Dropout Rate (2)
param_kMax

Parameter Description: Maximum Number of Stages
param_kappa

Parameter Description: Kappa
param_eventTime

Parameter Description: Event Time
param_typeOfShape

Parameter Description: Type Of Shape
param_dropoutTime

Parameter Description: Dropout Time
param_typeOfSelection

Parameter Description: Type of Selection
param_hazardRatio

Parameter Description: Hazard Ratio
param_piecewiseSurvivalTime

Parameter Description: Piecewise Survival Time
param_thetaH0

Parameter Description: Theta H0
param_includeAllParameters

Parameter Description: Include All Parameters
param_plannedEvents

Parameter Description: Planned Events
param_rValue

Parameter Description: R Value
param_seed

Parameter Description: Seed
param_threshold

Parameter Description: Threshold
param_successCriterion

Parameter Description: Success Criterion
plot.SummaryFactory

Summary Factory Plotting
plot.StageResults

Stage Results Plotting
param_normalApproximation

Parameter Description: Normal Approximation
param_sided

Parameter Description: Sided
plot.ParameterSet

Parameter Set Plotting
plot.SimulationResults

Simulation Results Plotting
param_nMax

Parameter Description: N_max
printCitation

Print Citation
param_palette

Parameter Description: Palette
print.SimulationResults

Print Simulation Results
param_stDevH1

Parameter Description: Standard Deviation Under Alternative
param_typeOfComputation

Parameter Description: Type Of Computation
param_minNumberOfSubjectsPerStage

Parameter Description: Minimum Number Of Subjects Per Stage
param_stDev

Parameter Description: Standard Deviation
param_slope

Parameter Description: Slope
param_typeOfDesign

Parameter Description: Type of Design
print.FieldSet

Print Field Set Values
param_maxNumberOfIterations

Parameter Description: Maximum Number Of Iterations
param_minNumberOfEventsPerStage

Parameter Description: Min Number Of Events Per Stage
param_median2

Parameter Description: Median (2)
print.ParameterSet

Print Parameter Set Values
rpact

rpact - Confirmatory Adaptive Clinical Trial Design and Analysis
param_tolerance

Parameter Description: Tolerance
plot.EventProbabilities

Event Probabilities Plotting
plot.NumberOfSubjects

Number Of Subjects Plotting
readDatasets

Read Multiple Datasets
resetLogLevel

Reset Log Level
param_theta

Parameter Description: Theta
testPackage

Test Package
t,FieldSet-method

Field Set Transpose
utilitiesForSurvivalTrials

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

Write Multiple Datasets
setLogLevel

Set Log Level
summary.ParameterSet

Parameter Set Summary
summary.TrialDesignSet

Trial Design Set Summary
readDataset

Read Dataset
utilitiesForPiecewiseExponentialDistribution

The Piecewise Exponential Distribution
test_plan_section

Test Plan Section
rawDataTwoArmNormal

Raw Dataset Of A Two Arm Continuous Outcome With Covariates
param_stratifiedAnalysis

Parameter Description: Stratified Analysis
param_showSource

Parameter Description: Show Source
param_plannedSubjects

Parameter Description: Planned Subjects
param_stageResults

Parameter Description: Stage Results
param_three_dots

Parameter Description: "..."
param_userAlphaSpending

Parameter Description: User Alpha Spending
param_showStatistics

Parameter Description: Show Statistics
param_three_dots_plot

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

Parameter Description: Plot Points Enabled
param_varianceOption

Parameter Description: Variance Option
plot.TrialDesign

Trial Design Plotting
writeDataset

Write Dataset
plot.Dataset

Dataset Plotting
plot.TrialDesignPlan

Trial Design Plan Plotting
plot.AnalysisResults

Analysis Results Plotting
[,TrialDesignSet-method

Access Trial Design by Index
setOutputFormat

Set Output Format
plot.TrialDesignSet

Trial Design Set Plotting
summary.AnalysisResults

Analysis Results Summary
summary.Dataset

Dataset Summary
print.Dataset

Print Dataset Values
AnalysisResultsGroupSequential

Analysis Results Group Sequential