Workshops: ISBA 2016, Introduction to Stan

Workshops: ISBA 2016, Introduction to Stan

The Stan project is in development since 2011 and aims to enable efficient Bayesian inference. This tutorial will focus on the foundations of Stan, introduce the Stan modeling language, explain how to do Bayesian inference with Stan and finally address best practices. These will be introduced using examples of increasing complexity ranging from logistic regression to hierarchical non-linear ODE models which will demonstrate the scalability and flexibility of Stan.

Stan’s key feature is the Hamiltonian MCMC sampler which is different than the various established flavors of Bayesian inference Using Gibbs Sampling (BUGS), such as WinBUGS, OpenBUGS, and JAGS. To fully exploit the advantages of Hamiltonian MCMC, participants will be briefly introduced to the foundations of Hamiltonian MCMC.

After these more theoretical aspects, the Stan modeling language will be introduced. The Stan modeling language is inspired by the BUGS family such that BUGS users can quickly adopt Stan. Most importantly, participants will be taught best practices to write efficient Stan models. This will include how to debug Stan models easily and what to consider in order to expedite Stan models. These best practices will be presented using examples of increasing complexity. The tutorial will include an interactive session with hands-on exercises.

Participants are encouraged to bring their fully charged laptop and install before the course the latest Stan, ideally download the excellent Stan reference manual along with it. We highly recommend the use of RStan which will be used for the demonstrations. The example data set for the exercises can be downloaded below. A more advanced example, which we will discuss, will be shared here before the course.


[1] Neuenschwander B, Capkun-Niggli G, Branson M, Spiegelhalter DJ. Summarizing historical information on controls in clinical trials. Clin Trials. 2010; 7(1):5-18