2019 Lecture/Exercise 3.3

Lecture/Exercise 4.1

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

Projection

Notes: R_BM_OUCH_minitutorial.pdf chapter 3

Code:

bmousim.R
OU.sim.branch.R

ou2drgl.R (optional, extra)

Audio recordings:

Lecture3-3a.WMA

Lecture3-3a.mp3

 

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

Lecture3-3b.WMA

Lecture3-3b.mp3

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