# The easiest way to get rpact is to install it from cran:
install.packages("rpact")rpact: Confirmatory Adaptive Clinical Trial Design, Simulation, and Analysis
A validated, open source, free-of-charge R software package
rpact is a comprehensive validated, open source, free-of-charge R software package for:
- Clinical trial planning
- Clinical trial design evaluation and simulation
- Clinical trial data 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
Installation from CRAN
Installation of the Developer Version
To install the latest rpact developer version, please follow the instructions described here.
Note that you or your organization must be an active RPACT SLA member to get access to the manual and the latest rpact developer version.
Learn To Use rpact
We recommend three ways to learn how to use rpact:
- Use the Shiny app: shiny.rpact.com
- Use the rpact vignettes
- Book a training: www.rpact.com/services
Vignettes
- The open access vignettes are hosted at www.rpact.org/vignettes
- The exclusive vignettes are hosted at www.rpact.com/vignettes
Online Help
The online documentation (help files) can be opened here: www.rpact.org/documentation
Additionally there are two different pdf versions of the manual available:
- rpact_v3_4.0_quick_start_guide.pdf (recommended for beginners)
- rpact_v3_4.0_manual.pdf
Inline Help
# display the manual of the package
help(package = "rpact")Getting Started
# load the package
library(rpact)
# display the manual of the package
help(package = "rpact")
# create an inverse normal design with default parameters
design <- getDesignInverseNormal()
# take a look at the design and its default values
design
# create a summary ouput of the design
summary(design)
# display the design characteristics
getDesignCharacteristics(design)
# plot the design with default type 1 (Boundary Plot)
plot(design)
# create an 'Average Sample Size and Power / Early Stop' plot
plot(design, type = 2, nMax = 12)Working with datasets
# create a group sequential design
design <- getDesignGroupSequential(
kMax = 4, alpha = 0.025,
informationRates = c(0.2, 0.5, 0.8, 1),
futilityBounds = rep(0.5244, 4 - 1),
typeOfDesign = "WT", deltaWT = 0.45
)
# take a look at the design
design
# create a dataset of means
data <- getDataset(
n1 = c(22, 11, 22, 11),
n2 = c(22, 13, 22, 13),
means1 = c(1, 1.1, 1, 1),
means2 = c(1.4, 1.5, 3, 2.5),
stds1 = c(1, 2, 2, 1.3),
stds2 = c(1, 2, 2, 1.3)
)
# display the stage results
getStageResults(design = design, dataInput = data, stage = 3)
# display the analysis results
getAnalysisResults(
design = design, dataInput = data, equalVariances = TRUE,
stage = stage, nPlanned = rep(10, kMax - stage),
thetaH0 = 0, thetaH1 = 1.3, allocationRatioPlanned = 2
)User Concept
Workflow
- Everything is starting with a design, e.g.:
design <- getDesignGroupSequential() - Find the optimal design parameters with help of rpact comparison tools:
getDesignSet - Calculate the required sample size, e.g.:
getSampleSizeMeans(),getPowerMeans() - Simulate specific characteristics of an adaptive design, e.g.:
getSimulationMeans() - Collect your data, import it into R and create a dataset:
data <- getDataset() - Analyze your data:
getAnalysisResults(design, data)
Focus on Usability
The most important rpact functions have intuitive names:
getDesign[GroupSequential/InverseNormal/Fisher]()getDesignCharacteristics()getSampleSize[Means/Rates/Survival]()getPower[Means/Rates/Survival]()getSimulation[MultiArm/Enrichment]`[Means/Rates/Survival]()`getDataSet()getAnalysisResults()getStageResults()
RStudio / Eclipse: auto code completion makes it easy to use these functions.
R generics
In general, everything runs with the R standard functions which are always present in R: so-called R generics, e.g., print, summary, plot, as.data.frame, names, length
Utilities
Several utility functions are available, e.g.
getAccrualTime()getPiecewiseSurvivalTime()getNumberOfSubjects()getEventProbabilities()getPiecewiseExponentialDistribution()- survival helper functions for conversion of
pi,lambdaandmedian, e.g.,getLambdaByMedian() testPackage(): installation qualification on a client computer or company server (via unit tests)
Validation
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.
About
- rpact is a comprehensive validated1 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.com/products
- 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/services
Contact
- For general requests please send an email to
- Please send your support request to
- Or use our contact form at www.rpact.com/contact
Bugs and Issues
Please use the github bug report form to submit bug descriptions and issues in a systematic way: github.com/rpact-com/rpact/issues
Recommended Vignette
Footnotes
The rpact validation documentation is available exclusively for our customers and supporting companies. For more information visit www.rpact.com/services/sla↩︎