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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 software development services
    • technical support for the rpact package
    • consultancy and user training for clinical research 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

3.3.0

License

LGPL-3

Maintainer

Friedrich Pahlke

Last Published

June 15th, 2022

Functions in rpact (3.3.0)

AnalysisResultsEnrichment

Basic Class for Analysis Results Enrichment
AnalysisResultsGroupSequential

Analysis Results Group Sequential
AnalysisResultsMultiArmFisher

Analysis Results Multi-Arm Fisher
AnalysisResultsEnrichmentInverseNormal

Analysis Results Enrichment Inverse Normal
AnalysisResultsFisher

Analysis Results Fisher
AnalysisResults

Basic Class for Analysis Results
AccrualTime

Accrual Time
AnalysisResultsConditionalDunnett

Analysis Results Multi-Arm Conditional Dunnett
AnalysisResultsMultiArm

Basic Class for Analysis Results Multi-Arm
AnalysisResultsInverseNormal

Analysis Results Inverse Normal
AnalysisResults_summary

Analysis Results Summary
FieldSet_names

Names of a Field Set Object
FieldSet

Field Set
SimulationResultsEnrichmentMeans

Class for Simulation Results Enrichment Means
Dataset

Dataset
FrameSet_as.matrix

Coerce Frame Set to a Matrix
FieldSet_print

Print Field Set Values
SimulationResultsEnrichmentRates

Class for Simulation Results Enrichment Rates
ConditionalPowerResults

Conditional Power Results
DatasetRates

Dataset of Rates
Dataset_summary

Dataset Summary
DatasetMeans

Dataset of Means
SimulationResultsMultiArmMeans

Class for Simulation Results Multi-Arm Means
SimulationResultsMultiArmRates

Class for Simulation Results Multi-Arm Rates
DatasetSurvival

Dataset of Survival Data
ClosedCombinationTestResults

Analysis Results Closed Combination Test
ParameterSet_print

Print Parameter Set Values
Dataset_print

Print Dataset Values
ParameterSet_as.data.frame

Coerce Parameter Set to a Data Frame
ParameterSet_summary

Parameter Set Summary
StageResultsMeans

Stage Results of Means
AnalysisResults_as.data.frame

Coerce AnalysisResults to a Data Frame
PiecewiseSurvivalTime

Piecewise Exponential Survival Time
SimulationResultsMeans

Class for Simulation Results Means
SimulationResultsEnrichmentSurvival

Class for Simulation Results Enrichment Survival
StageResultsSurvival

Stage Results of Survival Data
TrialDesignPlanSurvival

Trial Design Plan Survival
StageResultsRates

Stage Results of Rates
dataEnrichmentSurvival

Enrichment Dataset of Survival Data
TrialDesignPlan_as.data.frame

Coerce Trial Design Plan to a Data Frame
StageResults_as.data.frame

Coerce Stage Results to a Data Frame
ParameterSet

Parameter Set
AnalysisResultsMultiHypotheses

Basic Class for Analysis Results Multi-Hypotheses
NumberOfSubjects

Number Of Subjects
PlotSettings

Plot Settings
AnalysisResultsMultiArmInverseNormal

Analysis Results Multi-Arm Inverse Normal
StageResults_names

Names of a Stage Results Object
SummaryFactory

Summary Factory
dataEnrichmentSurvivalStratified

Stratified Enrichment Dataset of Survival Data
dataRates

One-Arm Dataset of Rates
EventProbabilities

Event Probabilities
PowerAndAverageSampleNumberResult

Power and Average Sample Number Result
SimulationResults_names

Names of a Simulation Results Object
TrialDesignCharacteristics

Trial Design Characteristics
SimulationResultsSurvival

Class for Simulation Results Survival
TrialDesign

Basic Trial Design
getData

Get Simulation Data
getNumberOfSubjects

Get Number Of Subjects
getConditionalRejectionProbabilities

Get Conditional Rejection Probabilities
dataSurvival

One-Arm Dataset of Survival Data
rcmd

Get Object R Code
AnalysisResults_names

Names of a Analysis Results Object
TrialDesignFisher

Fisher Design
TrialDesignSet

Class for trial design sets.
TrialDesignSet_as.data.frame

Coerce Trial Design Set to a Data Frame
SimulationResultsRates

Class for Simulation Results Rates
getPiecewiseSurvivalTime

Get Piecewise Survival Time
SimulationResultsMultiArmSurvival

Class for Simulation Results Multi-Arm Survival
getPlotSettings

Get Plot Settings
dataEnrichmentMeans

Enrichment Dataset of Means
PowerAndAverageSampleNumberResult_as.data.frame

Coerce Power And Average Sample Number Result to a Data Frame
TrialDesignGroupSequential

Group Sequential Design
SimulationResults

Class for Simulation Results
StageResults

Basic Stage Results
dataEnrichmentMeansStratified

Stratified Enrichment Dataset of Means
SimulationResults_print

Print Simulation Results
getDesignConditionalDunnett

Get Design Conditional Dunnett Test
getDesignGroupSequential

Get Design Group Sequential
dataMeans

One-Arm Dataset of Means
dataMultiArmMeans

Multi-Arm Dataset of Means
getDesignFisher

Get Design Fisher
getPowerAndAverageSampleNumber

Get Power And Average Sample Number
getLongFormat

Get Long Format
getLogLevel

Get Log Level
dataEnrichmentRates

Enrichment Dataset of Rates
dataEnrichmentRatesStratified

Stratified Enrichment Dataset of Rates
plotTypes

Get Available Plot Types
getClosedConditionalDunnettTestResults

Get Closed Conditional Dunnett Test Results
getFinalConfidenceInterval

Get Final Confidence Interval
getClosedCombinationTestResults

Get Closed Combination Test Results
getConditionalPower

Get Conditional Power
getFinalPValue

Get Final P Value
getSimulationEnrichmentMeans

Get Simulation Enrichment Means
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.
getDesignInverseNormal

Get Design Inverse Normal
getPowerRates

Get Power Rates
getObservedInformationRates

Get Observed Information Rates
getOutputFormat

Get Output Format
getPowerMeans

Get Power Means
getSampleSizeMeans

Get Sample Size Means
getRepeatedPValues

Get Repeated P Values
getSimulationMeans

Get Simulation Means
getRawData

Get Simulation Raw Data for Survival
getRepeatedConfidenceIntervals

Get Repeated Confidence Intervals
param_activeArms

Parameter Description: Active Arms
getPowerSurvival

Get Power Survival
kable.ParameterSet

Create output in Markdown
param_accrualIntensityType

Parameter Description: Accrual Intensity Type
getWideFormat

Get Wide Format
getSimulationEnrichmentRates

Get Simulation Enrichment Rates
param_accrualTime

Parameter Description: Accrual Time
param_calcSubjectsFunction

Parameter Description: Calculate Subjects Function
param_adaptations

Parameter Description: Adaptations
param_effectList

Parameter Description: Effect List
param_design_with_default

Parameter Description: Design with Default
param_design

Parameter Description: Design
param_dropoutTime

Parameter Description: Dropout Time
param_informationRates

Parameter Description: Information Rates
param_intersectionTest_Enrichment

Parameter Description: Intersection Test
param_legendPosition

Parameter Description: Legend Position On Plots
param_nMax

Parameter Description: N_max
param_lambda2

Parameter Description: Lambda (2)
TrialDesignPlan

Basic Trial Design Plan
TrialDesignInverseNormal

Inverse Normal Design
TrialDesignCharacteristics_as.data.frame

Coerce TrialDesignCharacteristics to a Data Frame
kable

Create tables in Markdown
getSimulationMultiArmMeans

Get Simulation Multi-Arm Means
TrialDesignConditionalDunnett

Conditional Dunnett Design
TrialDesignSet_names

Names of a Trial Design Set Object
TrialDesignPlanRates

Trial Design Plan Rates
TrialDesignSet_length

Length of Trial Design Set
param_conditionalPower

Parameter Description: Conditional Power
param_dropoutRate1

Parameter Description: Dropout Rate (1)
TrialDesignPlanMeans

Trial Design Plan Means
getSimulationMultiArmRates

Get Simulation Multi-Arm Rates
getSimulationEnrichmentSurvival

Get Simulation Enrichment Survival
param_gED50

Parameter Description: G ED50
param_plannedEvents

Parameter Description: Planned Events
param_accrualIntensity

Parameter Description: Accrual Intensity
TrialDesign_as.data.frame

Coerce TrialDesign to a Data Frame
param_nPlanned

Parameter Description: N Planned
getAnalysisResults

Get Analysis Results
getAccrualTime

Get Accrual Time
getDataset

Get Dataset
param_pi1_survival

Parameter Description: Pi (1) for Survival Data
param_grid

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

Parameter Description: Pi (2) for Rates
param_median1

Parameter Description: Median (1)
param_lambda1

Parameter Description: Lambda (1)
param_kappa

Parameter Description: Kappa
param_median2

Parameter Description: Median (2)
Trial_Design_Set_summary

Trial Design Set Summary
dataMultiArmSurvival

Multi-Arm Dataset of Survival Data
dataMultiArmRates

Multi-Arm Dataset of Rates
param_stratifiedAnalysis

Parameter Description: Stratified Analysis
param_three_dots_plot

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

Parameter Description: Select Populations Function
param_showSource

Parameter Description: Show Source
param_dropoutRate2

Parameter Description: Dropout Rate (2)
param_plannedSubjects

Parameter Description: Planned Subjects
getDesignCharacteristics

Get Design Characteristics
param_successCriterion

Parameter Description: Success Criterion
getSimulationMultiArmSurvival

Get Simulation Multi-Arm Survival
param_bindingFutility

Parameter Description: Binding Futility
param_threshold

Parameter Description: Threshold
param_directionUpper

Parameter Description: Direction Upper
param_digits

Parameter Description: Digits
param_calcEventsFunction

Parameter Description: Calculate Events Function
getEventProbabilities

Get Event Probabilities
getDesignSet

Get Design Set
param_groups

Parameter Description: Number Of Treatment Groups
param_hazardRatio

Parameter Description: Hazard Ratio
printCitation

Print Citation
getLambdaStepFunction

Get Lambda Step Function
getParameterCaption

Get Parameter Caption
getGroupSequentialProbabilities

Get Group Sequential Probabilities
param_kMax

Parameter Description: Maximum Number of Stages
param_maxInformation

Parameter Description: Maximum Information
param_intersectionTest_MultiArm

Parameter Description: Intersection Test
rawDataTwoArmNormal

Raw Dataset Of A Two Arm Continuous Outcome With Covariates
param_maxNumberOfEventsPerStage

Parameter Description: Max Number Of Events Per Stage
param_palette

Parameter Description: Palette
getSampleSizeSurvival

Get Sample Size Survival
getSampleSizeRates

Get Sample Size Rates
getParameterName

Get Parameter Name
getSimulationRates

Get Simulation Rates
param_plotSettings

Parameter Description: Plot Settings
param_plotPointsEnabled

Parameter Description: Plot Points Enabled
param_pi1_rates

Parameter Description: Pi (1) for Rates
param_maxNumberOfIterations

Parameter Description: Maximum Number Of Iterations
getSimulationSurvival

Get Simulation Survival
param_varianceOption

Parameter Description: Variance Option
plot.AnalysisResults

Analysis Results Plotting
plot.TrialDesign

Trial Design Plotting
plot.SummaryFactory

Summary Factory Plotting
param_allocationRatioPlanned

Parameter Description: Allocation Ratio Planned
param_alternative_simulation

Parameter Description: Alternative for Simulation
getStageResults

Get Stage Results
getTestActions

Get Test Actions
param_niceColumnNamesEnabled

Parameter Description: Nice Column Names Enabled
param_maxNumberOfSubjects

Parameter Description: Maximum Number Of Subjects
param_allocationRatioPlanned_sampleSize

Parameter Description: Allocation Ratio Planned With Optimum Option
setLogLevel

Set Log Level
param_alpha

Parameter Description: Alpha
param_seed

Parameter Description: Seed
param_rValue

Parameter Description: RValue
setOutputFormat

Set Output Format
param_normalApproximation

Parameter Description: Normal Approximation
param_populations

Parameter Description: Populations
param_selectArmsFunction

Parameter Description: Select Arms Function
param_stDevH1

Parameter Description: Standard Deviation Under Alternative
param_theta

Parameter Description: Theta
param_alternative

Parameter Description: Alternative
param_conditionalPowerSimulation

Parameter Description: Conditional Power
param_stDevSimulation

Parameter Description: Standard Deviation for Simulation
param_beta

Parameter Description: Beta
param_thetaH0

Parameter Description: Theta H0
plot.Dataset

Dataset Plotting
plot.EventProbabilities

Event Probabilities Plotting
plot.SimulationResults

Simulation Results Plotting
param_stage

Parameter Description: Stage
plot.StageResults

Stage Results Plotting
param_typeOfDesign

Parameter Description: Type of Design
param_stageResults

Parameter Description: Stage Results
param_typeOfSelection

Parameter Description: Type of Selection
param_eventTime

Parameter Description: Event Time
param_dataInput

Parameter Description: Data Input
param_minNumberOfEventsPerStage

Parameter Description: Min Number Of Events Per Stage
param_epsilonValue

Parameter Description: EpsilonValue
plot.NumberOfSubjects

Number Of Subjects Plotting
t,FieldSet-method

Field Set Transpose
[,TrialDesignSet-method

Access Trial Design by Index
readDatasets

Read Multiple Datasets
readDataset

Read Dataset
plot.ParameterSet

Parameter Set Plotting
param_minNumberOfSubjectsPerStage

Parameter Description: Minimum Number Of Subjects Per Stage
param_effectMatrix

Parameter Description: Effect Matrix
utilitiesForSurvivalTrials

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

Parameter Description: Effect Measure
writeDataset

Write Dataset
param_informationEpsilon

Parameter Description: Information Epsilon
param_stDev

Parameter Description: Standard Deviation
param_includeAllParameters

Parameter Description: Include All Parameters
param_maxNumberOfSubjects_survival

Parameter Description: Maximum Number Of Subjects For Survival Endpoint
param_slope

Parameter Description: Slope
param_thetaH1

Parameter Description: Effect Under Alternative
param_maxNumberOfSubjectsPerStage

Parameter Description: Maximum Number Of Subjects Per Stage
param_three_dots

Parameter Description: "..."
param_pi2_survival

Parameter Description: Pi (2) for Survival Data
param_piecewiseSurvivalTime

Parameter Description: Piecewise Survival Time
param_showStatistics

Parameter Description: Show Statistics
plot.TrialDesignSet

Trial Design Set Plotting
param_typeOfComputation

Parameter Description: Type Of Computation
plot.TrialDesignPlan

Trial Design Plan Plotting
param_tolerance

Parameter Description: Tolerance
resetLogLevel

Reset Log Level
rpact

rpact - Confirmatory Adaptive Clinical Trial Design and Analysis
param_sided

Parameter Description: Sided
testPackage

Test Package
utilitiesForPiecewiseExponentialDistribution

The Piecewise Exponential Distribution
param_typeOfShape

Parameter Description: Type Of Shape
param_userAlphaSpending

Parameter Description: User Alpha Spending
writeDatasets

Write Multiple Datasets