phytools @ Anthrotree 2014

Lecture PDFs

Ancestral character estimation for discrete & continuous characters.PDF
Analyzing discrete & contintuous characters on phylogenies: The threshold modelPDF
Plotting comparative data & phylogenies.PDF


All of the following exercises were built using the knitr R package.

Ancestral character estimation I: Continuous charactersURL
Ancestral character estimation II: Discrete charactersURL
Analyzing discrete & continuous characters using the threshold modelURL
Plotting comparative data & treesURL

phytools package builds

A tiny fraction of the exercises require a non-CRAN phytools version (i.e., a very recent version of phytools with some updates that is not yet on CRAN). If you can install packages from source, or are working with the latest R release in Windows, you can install one of the following two versions:

Package versionLink
phytools package source (for phytools installation from source)phytools_0.4-11.tar.gz
phytools Windows binary (for phytools installation in Windows with R>=3.0)

Written by Liam J. Revell. Last updated May 30, 2014