Phylogenetic Comparative Methods in R Workshop

Taught by Marguerite Butler, Michael Alfaro, and Samantha Price
Presented at 2009 SICB meeting in Boston
Sponsored by Division of Evolution and Systematic Biology of SICB, NSF, and NESCENT

R is a powerful, free(!), high-level statistical computing language that is an excellent computing environment for analysis of data.
Recently, many packages have been developed to conduct evolutionary analyses.

Day 1: Intro to R

Users completely new to the language were introduced to the powerful features of R and provided with a solid yet basic introduction to the langauage so that they could quickly get up and running. Topics covered included:

* objects (how R organizes data) and how to manipuate them
* naming and manipulating objects,
* plotting
* functions
* sessions
* packages
* finding help.

Day 2: Intro to Comparative Methods in R

Workshop attendees were introduced to phylogenetic analysis and features available in R, with a focus on practical examples:

* overview of Comparative Methods
* independent contrasts analysis
* testing adaptation using OUCH (Ornstein Uhlenbeck for Comparative Analysis)
* test for correlation of traits on a tree or across a distribution of tree under different evolutionary models
* reconstruct ancestral states
* examine correlated patterns of trait evolution and lineage diversification
* calculate disparity and disparity through time plots
* simulate character evolution.
* create publication-quality plots of trees and graphs

Course Materials

Dowload everything at once: course material directory (.tar.gz file; unpack this with unstuffit, winzip, or simlar software)

If that fails, download by clicking on each file here.

Packages Used


Instructors: Michael Alfaro (UCLA, michaelalfaro at is an evolutionary biologist studying morphological evolution and species diversification in fishes. Marguerite Butler (University of Hawaii, mbutler at studies comparative physiology and morphological evolution in lizards and damselflies and is a contributor to the OUCH package for Ohrnstein-Uhlenbeck analyses in R. Samantha A. Price (UC Davis, saprice at studies comparative macroevolution in mammals and morphological diversification in fishes.

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