16.11.2021
Exercises demonstrating mcmc-diversitree, PyRate (the BDC model), and fossilBM.
mcmc-diversitree is a Bayesian implementation of the SSE models (state speciation extinction; Maddison et al 2007 Sys Biol) using the R package 'diversitree' (FitzJohn 2009 Sys Biol).
PyRate is a Python program implementing various birth-death models applied to fossil occurrence data (and phylogenies) in a Bayesian framework (Silvestro et al. 2018 Nature Comm, 2019 Paleobiology).
fossilBM is an R program implementing models of trait evolution in a Bayesian framework inferred from phylogenies with fossils (Silvestro et al. 2018 Sys Biol; Zhang et al. 2021 Sys Biol).