Evolutionary and Ecological Analyses using Phylogenies in R
There will be four 2-hour sessions in May 2010: Mon. 10th , Wed.12th, Mon. 17th and
Wed. 19th at 4:10 - 6:30pm.
We have designed each session to be standalone, so feel free to just attend the day(s) or
session(s) that interest you. HOWEVER, please let us know when you hope to attend so
we can estimate the size of classroom that is needed. If you are not familiar with ‘R’
please attend the introductory session on the first day as that is the only time we will be
covering the basics.
Day 1- May 10th
1st session (4:10 - 5:10 pm): Basic Introduction
 How to load packages
 Basic interface
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Loading data
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Calculations
Setting paths/finding files
.csv, .txt
Headers
Missing data
Formats (vectors, dataframes)
Manipulating data
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Subsetting rows/columns
2nd session (5:30 - 6:30 pm): Introduction to using Phylogenies
Packages: Ape & apTreeshape
 Introduction to phylogenetic packages in R
 Reading and manipulating trees
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Opening newick and nexus trees
Introduction to phylo format
Plotting trees
Pruning trees
Other tree manipulations
Day 2- May 12th
1st session (4:10 - 5:10 pm): Speciation & Diversification
Packages: Laser, Geiger, Ape, apTreeshape & Diversitree
 Lineage through time plots
 Tree statistics (gamma statistic – Pybus & Harvey etc.)
 Laser
 Simulating trees (Yule and Birth/Death)
 MEDUSA – shifts in diversification rates (in Gieger)
 BISSE in R (source code only not on CRAN)
2nd session (5:30 - 6:30 pm): Discrete data
Packages: Ape & Geiger
 Ancestral state reconstruction
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
Fitting models of evolution (fitDiscrete in Geiger)
Day 3- May 17th
1st session (4:10 - 5:10 pm): Continuous data
Packages: Ape, Geiger, CAIC in R
 Ancestral state reconstruction
 Fitting models of evolution (fitContinuous in Geiger)
 Correlated evolution – Independent Contrasts
 Simulating traits under Brownian motion
2nd session (5:30 - 6:30 pm): Continuous data
Packages: OUCH
 Getting your trees and data into OUCH format
 Comparing Ornstein-Uhlenbeck (OU) models of evolution
 Simulating traits under OU
Day 4- May 19th
1st session (4:10 - 5:10 pm): Phyloecology
Packages: Picante
 Testing for phylogenetic signal in trait data
 Calculating phylogenetic dispersion of communities
 Randomization tests
2nd session (5:30 - 6:30 pm): Plotting figures – or requested topic(s)
Packages: Ape
 Simple trees with nodal values
 Visualizing data on the tips of trees
 Visualizing ancestral state reconstructions
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Resources for learning R
Online Resources:
first, check out http://cran.r-project.org/
Selected resources:
An Introduction to R: http://cran.r-project.org/doc/manuals/R-intro.pdf
Statistics Using R with Biological Examples: http://cran.rproject.org/doc/contrib/Seefeld_statsrbio.pdf
Practical Regression and Anova using R: http://cran.r-project.org/doc/contrib/FarawayPRA.pdf
R Reference Card: http://cran.r-project.org/doc/contrib/Short-refcard.pdf
Books: a partial list at http://www.r-project.org/doc/bib/R-books.html
The most up-to-date book on using R for phylogenetic
Analysis of Phylogenetics and Evolution with R Paradis, Emmanuel Springer, 2006. This
book is available as free download through UC subscription to Springer at:
http://www.springerlink.com/content/978-0-387-32914-7
Other “SimpleR” books are available as free downloads from Springer at
http://www.springerlink.com/content/t83625/?p=4c6cda22762140f6a15f6cac9fbfe592&p
i=0 including:
Interactive and Dynamic Graphics for Data Analysis With R and Ggobi. Dianne
Cook and Deborah F. Swayne. Springer, 2006.
Introducing Monte Carlo Methods with R. Christian Robert and George Casella.
Springer, 2006.
Multivariate Data Visualization with R. Deepayan Sarkar. Springer, 2006.
Morphometrics with R. Julien Claude Springer, 2006.
A Primer of Ecology with R. M. Henry Stevens. Springer, 2006.
Applied Statistical Genetics with R For Population-based Association Studies.
Andrea S. Foulkes. Springer, 2006
Bayesian Computation with R. Jim Albert. Springer, 2006
A Beginner's Guide to R. Alain F. Zuur, Elena N. Ieno and Erik Meesters.
Springer, 2006
Data Manipulation with R. Phil Spector. Springer, 2006
The Statistics of Gene Mapping David Siegmund and Benjamin Yakir. Springer,
2007
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Basic intro
The R Book Michael Crawley 2007, Wiley
R Graphics Paul Murrell, Chapman & Hall/CRC 2005
Other related books:
Computational Genome Analysis An Introduction Deonier, Richard C., et al. Springer,
2007
Bioinformatics and Computational Biology Solutions Using R… Gentleman, R et al.
Springer, 2005
Bioinformatics with R. Robert Gentleman. Chapman & Hall/CRC, 2008
Packages’ manuals and instructions:
Each R package (extension) comes with a manual, often with example data, and
sometimes with a tutorial. The quality of the above changes a lot. They are made and
maintained by the authors. The manual entry for each command in R is identical to the
instruction that pop up when typing help(command). Manuals are found on CRAN’s
website, under each package’s homepage.
One can find a package that runs a statistical test by searching a test name or properties in
CRAN. For phylogenetic methods, a page summarizing all available packages (including
some that are not hosted on CRAN) and their main functions is maintained by Brian
O’Meara at http://cran.r-project.org/web/views/Phylogenetics.html. Links are provided
for each package.
R-sig-phylo r-sig-phylo@r-project.org: a mailing list dealing with any R-phylogenetic
related issues. Subscribers are very responsive and helpful. Be sure to include your code
and data when posting questions (list does not accept attachments).
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