Practice

'Mugration' models

There are several libraries in R that allow the modeling of a categorical trait on a fixed tree
- ace in the library ape
- make.simmap in the library phytools performs stochastic character mapping
BEAST allows the joint estimation of trees and traits

Structured coalescent models can be fitted in R using the rcolgem library
Currently beyond the scope of this course, but please see the vignettes in the rcolgem package