OU processes on phylogenies and their interpretation
Marguerite Butler and Brian O’Meara
Butler: Testing Hypotheses of Evolution by Varying the Model
Learning Objectives:
- Gain appreciation for how models can be used to test evolutionary hypotheses
- Building intuition about BM and OU processes by making your own simulations
- adding stochastic components to trait values through discrete time (sigma)
- adding trends toward optimal values (theta and alpha)
- adding branching
- changing the parameters along the tree
Notes: R_BM_OUCH_minitutorial.pdf chapter 3
Code:
ou2drgl.R (optional, extra)
Audio recordings:
O’Meara:
Learning objectives
- Understand connection between OU methods
- Be able to compare models
- Understand potential problems with your particular analysis (more on this tomorrow)
- Parameter estimation for the win!
R packages
OUwie: install.packages(“OUwie”) or bleeding edge remotes::install_github(“thej022214/OUwie”).
Lecture projections
Presentation: PDF and PowerPoint
Exercise materials
O’Meara: Exercise and Answers
Audio recording