SISMID 2026 · Pre-session materials 2
Introduction to MCMC 2
Please complete all materials below before your first synchronous session.
The materials on this page should be reviewed before your live lab sessions on June 22 and June 23. Work through the videos, readings, and problem sets at your own pace.
Pre-session materials — Page 2
Pre-Course Work 3
Case Study 1: Serial Interval
Case Study 2: Poisson and NB Processes
Case Study 3: SIR and R0
Practical 6
Case Study 4: Metapopulation
Practical 7
Readings
Minin, Volodymyr — Introduction to Rstan
Gabry et al. (2019)
Visualization in Bayesian workflow. J. R. Statist. Soc. A 182, Part 2, pp. 389–402.
Hefferman, Smith & Wahl (2005)
Perspectives on the basic reproductive ratio. J R Soc Interface. Jun 7; 2(4): pp. 281–293. doi: 10.1098/rsif.2005.0042
Meyer, Held & Hohle (2017)
Spatio-temporal analysis of epidemic phenomena using the R package surveillance. Journal of Statistical Software, 77(11), pp. 1–55.
Wallinga & Lipsitch (2006)
How generation intervals shape the relationship between growth rates and reproductive numbers. Proc. R. Soc. B, 274, pp. 599–604. doi:10.1098/rspb.2006.3754
White & Pagano (2008)
A likelihood-based method for real-time estimation of the serial interval and reproductive number of an epidemic. Stat Med. 27(16): pp. 2999–3016. doi:10.1002/sim.3136.
Optional: What is Hamiltonian Monte Carlo?
If you are curious about Hamiltonian Monte Carlo, these two YouTube videos are highly recommended:
Video 1
Video 2
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