Welcome to the PhylogeogRaphy workshop (with BEAST2)!
Sessions are split into roughly two-hour chunks that align with typical start/end times of classes, and are meant to be as self-contained as possible – so, feel free to come and go as necessary! All materials will posted here for you to catch up on content if desired.
Participants should bring their own laptops for hands-on exercises.
For specific requirements, see the Requirements for workshop page.
Pre-workshop instructions
Topics and agenda
Monday
[September 29, 2025]
Monday: Discrete trait analysis I in R
Introduction, ancestral character estimation, and stochastic character mapping
Wednesday
[October 1, 2025]
Wednesday: Discrete trait analysis II in R
Birth-death models, state-dependent speciation and extinction (SSE) models
Thursday
[October 2, 2025]
Thursday: Phylodynamics I in R and BEAST2
Phylodynamics models (multi-type birth-death models, structured coalescents), and analysis in BEAST2
Friday
[October 3, 2025]
Friday: Phylodynamics II in BEAST2
Analysis in BEAST2 and advanced topics (Bayesian stochastic search variable selection)
