OncoBayes2: OncoBayes2

In OncoBayes2: Bayesian Logistic Regression for Oncology Dose-Escalation Trials

OncoBayes2

Description

Bayesian logistic regression model with optional EXchangeability-NonEXchangeability parameter modelling for flexible borrowing from historical or concurrent data-sources. The safety model can guide dose-escalation decisions for adaptive Oncology phase I dose-escalation trials which involve an arbitrary number of drugs.

Global Options

Option	Default	Description
OncoBayes2.MC.warmup	1000	MCMC warmup iterations
OncoBayes2.MC.iter	2000	total MCMC iterations
OncoBayes2.MC.save_warmup	TRUE	save warmup samples
OncoBayes2.MC.chains	4	MCMC chains
OncoBayes2.MC.thin	1	MCMC thinning
OncoBayes2.MC.control	⁠list(adapt_delta=0.99,⁠	sets control argument for Stan call
	stepsize=0.1)
OncoBayes2.MC.backend	rstan	Backend used to run Stan (rstan or cmdstanr)
OncoBayes2.abbreviate.min	0	Minimal length of variable names
		when abbreviating variable names.
		The default 0 disables abbreviation.

Author(s)

Maintainer: Sebastian Weber [e-mail]

Authors:

• Sebastian Weber [e-mail]

• Lukas A. Widmer [e-mail]

• Andrew Bean [e-mail]

Other contributors:

• Novartis Pharma AG [copyright holder]

• Trustees of Columbia University (R/stanmodels.R, configure, configure.win) [copyright holder]

References

\insertRef

neuenschwander2016codataOncoBayes2

\insertRef

neuenschwander2016exnexOncoBayes2

\insertRef

neuenschwander2008OncoBayes2

\insertRef

neuenschwander2014OncoBayes2

Stan Development Team (2024). RStan: the R interface to Stan. R package version 2.32.6. https://mc-stan.org

See Also

Useful links:

• https://opensource.nibr.com/OncoBayes2/

• Report bugs at https://github.com/Novartis/OncoBayes2/issues

OncoBayes2 documentation built on Aug. 5, 2026, 1:08 a.m.