Overview
We will meet twice weekly for about 90 minutes each session.
On Tuesdays there will be a lecture followed by a discussion. Make sure to do the required reading before coming to class.
On Thursdays there will be a computer activity, typically using R. Please have the most current version of R installed, as well as all listed packages.
Grades will be based on class participation and the presentation and results of your individual projects.
Schedule
Lectures and discussions |
Computer exercisesAug. 24: Introduction to R.
Code from day 1: codeday1.r |
Aug. 29: Introduction to macroevolutionary questions. Readings: Book chapter 1. Pennell and Harmon 2013.
|
Aug 31: Basics of reading and using trees in R.
Packages: ape, geiger, phytools; script; data files |
Sept. 7: Calculating and maximizing likelihoods.
Packages: ape, geiger; prep script (extra stuff!); class script |
Sept. 19: Multidimensional Brownian motion.
Readings: Book chapter 5. |
Sept. 21. Finish MCMC exercise from last week. Full script.
|
Sept. 28. Testing for evolutionary correlations: PICs and PGLS. Data files. In-class script.
|
Oct. 3: Discrete trait models.
Readings: Book chapter 7. |
Oct. 5: Exploring caudata. Introduction. Data is here. Files that start with "caud"
|
Oct. 17: Multi-rate and multi-regime discrete models.
Readings: Book chapter 9. |
Oct. 19: Fitting more complex models of trait evolution.
Packages: ape, geiger, ratematrix, geomorph, surface, bayou |
Oct. 24: Birth-death models
Readings: Book chapter 10, 11 |
Oct. 26: Simulating birth and death.
Packages: ape, geiger |
Oct. 31: Complex birth-death models
Readings: Book chapter 12 |
Nov. 2: Using BAMM.
Packages: BAMMtools (you also need BAMM) |
Nov. 7: State-dependent models
Readings: Book chapter 13 |
Nov. 9: Fitting state-dependent models.
Packages: diversitree |
Nov. 14: The state of comparative methods
Readings: |
Nov. 16: Debate
Details TBA |
Nov. 21: Fall break
|
Nov. 23: Fall break
|
Nov. 28: Finish projects
|
Nov. 30: Finish projects
|
Dec. 5: Presentations I
|
Dec. 7: Presentations II
|