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. |
References
Neuenschwander B, Roychoudhury S, Schmidli H (2016). “On the use of co-data in clinical trials.” Statistics in Biopharmaceutical Research, 8(3), 345–354. doi:10.1080/19466315.2016.1174149 .
Neuenschwander B, Wandel S, Roychoudhury S, Bailey S (2016). “Robust exchangeability designs for early phase clinical trials with multiple strata.” Pharmaceutical Statistics, 15(2), 123–134. doi:10.1002/pst.1730 .
Neuenschwander B, Branson M, Gsponer T (2008). “Critical aspects of the Bayesian approach to phase I cancer trials.” Statistics in Medicine, 27(13), 2420–2439. doi:10.1002/sim.3230 .
Neuenschwander B, Matano A, Tang Z, Roychoudhury S, Wandel S, Bailey S (2014). “A Bayesian Industry Approach to Phase I Combination Trials in Oncology.” In Statistical Methods in Drug Combination Studies, volume 69. CRC Press. doi:10.1201/b17965-9 .
Stan Development Team (2024). RStan: the R interface to Stan. R package version 2.32.6. https://mc-stan.org
Author
Maintainer: Sebastian Weber sebastian.weber@novartis.com
Authors:
Sebastian Weber sebastian.weber@novartis.com
Lukas A. Widmer lukas_andreas.widmer@novartis.com
Andrew Bean andrew.bean@novartis.com
Other contributors:
Novartis Pharma AG [copyright holder]
Trustees of Columbia University (R/stanmodels.R, configure, configure.win) [copyright holder]