Introduction

R integration with Cytel’s products provides a highly efficient way to create custom adaptive clinical trial designs and enhance your simulation capabilities, without requiring you to develop an entire R code base.

CyneRgy provides documentation, templates, examples, and R functions for integrating R with Cytel products such as East Horizon.

Important (January 2026): ArrivalTime is a new required parameter for the Response integration point. Existing R scripts must be updated to include this parameter in the function definition, even if it is not used. See Integration Point: Response for more information.

Getting Started

For a quick start, visit the Getting Started section. This guide covers the basics of integrating your R scripts with Cytel’s products, including detailed steps for accessing integration points, what input variables are available, what output variables are expected, and links to related templates and examples.

Examples and Templates

A variety of examples highlighting how R scripts integrate with Cytel’s simulation tools can be found in inst/Examples. Please see the Examples Outline for the complete list and descriptions. Each example includes a description and R scripts; some also include supporting files, practice scripts, and an optional RStudio project.

After installing CyneRgy, you can list or open examples. For example:

CyneRgy::RunExample()                                # Lists all available examples
CyneRgy::RunExample("TreatmentSelection")            # Opens the example project/folder in your IDE
CyneRgy::RunExample("GeneratePoissonArrival")
CyneRgy::RunExample("2ArmPatientDropout")
CyneRgy::RunExample("TreatmentSelection", strDirectory = getwd())   # Copy to a specific folder

RunExample() creates a writable copy when needed, then opens the description and R scripts in the active supported IDE. Use strDirectory to choose the copy location.

Templates are available in the Templates directory, and exploratory, in-progress examples can be found in the Sandbox directory. Note that Sandbox examples are incomplete and untested.

Functions

The package exports selected common functions for trial operations and binary, continuous, repeated-measures, time-to-event, DEP, and MEP endpoints. It also provides RunExample(), CreateCyneRgyFunction(), CreateCyneRgyExample(), and CombineAllRFiles() for working with examples and integration scripts. See the function reference for details.

Common functions can be called directly with CyneRgy::FunctionName(). A few examples:

# Arrival
CyneRgy::GeneratePoissonArrival( NumSub = 20, NumPrd = 1, PrdStart = 0, AccrRate = 10 )

# Randomization
CyneRgy::RandomizationSubjectsUsingUniformDistribution( NumSub = 20, NumArms = 2, AllocRatio = 1 )

# Dropout
CyneRgy::GenerateCensoringUsingBinomialProportion( NumSub = 20, ProbDrop = 0.1 )

# Binary endpoint analysis
CyneRgy::AnalyzeUsingPropTest(
    SimData     = data.frame( Response = c( 1, 0, 1, 1, 0, 0, 1, 0 ), TreatmentID = c( 0, 0, 0, 0, 1, 1, 1, 1 ) ),
    DesignParam = list( TailType = 1, CriticalPoint = 1.96 )
)

Installation

Currently, this package is not officially released and is not available on CRAN. However, it may be installed directly from GitHub using the remotes package with the following code:

remotes::install_github( "Cytel-Inc/CyneRgy@main" )

You must have the remotes package to use the command above. The optional rstudioapi package provides the best opening experience in RStudio and Positron; it is not required to list, locate, or copy examples.