Getting Started
Software and other preparations
Let’s make sure you have everything you need to get off to a good start!
The tutorials included in this Bayesian Intro will provide hands-on experience with Bayesian modelling for beginners using free and open source software–Stan and R. We use Stan because it is fast, flexible, well documented, and supported by an active community of developers and users (see Reading section). Note that we use R, but Stan also has support for Python, Julia, MATLAB, and command line interfaces, among others (see Stan Toolkit).
Software
Before we get started, let’s make sure that you have the right software installed on your computer. If you want to skip the installation and simply read along with the exercises, you can go ahead to the next section(s) now. When you’re ready to run code on your own computer, just come back to this page to find links to the required software.
You will need the following software to be able to run the example code on your own computer:
- R and RStudio or Positron (or your favourite R IDE)
- Getting Started with CmdStanR. (Note: Be sure to complete the Introduction and Installing CmdStan sections).
Reading
Bayesian Statistics
- Statistical Rethinking Lectures (and book) by Richard McElreath
- Bayes Rules! by Johnson, Ott, and Dogucu.
Stan Software
- Introductory Stan tutorials, videos, and podcasts
- Stan Documentation
- Stan User Forums
- Stan Case Studies
- Stan website (collects all of the above together, with some deeper-dive materials as well)
- Stan Toolkit
Books
- Gelman A, Carlin JB, Stern HS, Dunson DB, Vehtari A, Rubin D. 2015. Bayesian Data Analysis. Chapman & Hall/CRC Texts in Statistical Science. https://sites.stat.columbia.edu/gelman/book/BDA3.pdf
- McElreath R. 2015. Statistical Rethinking: A Bayesian course with examples in R and Stan. Chapman & Hall/CRC Texts in Statistical Science. https://civil.colorado.edu/~balajir/CVEN6833/bayes-resources/RM-StatRethink-Bayes.pdf
- Lambert B. A student’s guide to Bayesian statistics. Sage. https://study.sagepub.com/lambert.
- Hobbs NT, Hooten MB. 2015. Bayesian Models: A statistical primer for ecologists. Princeton University Press. Request full text pdf from authors via ResearchGate: https://www.researchgate.net/publication/283813602_Bayesian_Models_A_Statistical_Primer_for_Ecologists.