Half-day Workshop on Phylogenetic Comparative Methods
2024-11-11
1 About
This document consist in an introduction to the comparative methods. It contains theory as well as practical examples in R on Phylogenetic Generalized Least Squares (PGLS). It was developed for a half-day workshop that consists in short presentations followed by R exercises. Note that the present document should pretty much stand by itself because most of the theory given in the presentations are incorporated into the theory sections. Therefore, this document should contain all the necessary information to understand the examples.
I assume that the readers are “reasonably” familiar with R as well as with linear regression and its assumptions. There are a lot of good R introductory tutorials on the web and for linear models. Zuur et al. (Zuur et al. 2007) provide a good introduction to linear models, mixed-effects models and model comparison. Good introductions to model fitting in R can also be found on Dolph Schluter’s webpage and among the QCBS workshops.
1.1 Useful resources
The links below might provide additional information of interest.
Luke Harmon’s book - Phylogenetic Comparative Methods
Liam Revell’s blog on phylogenetic tools in R
Liam Revell and Luke Harmon book on Phylogenetic comparative methods in R
The list of R packages for phylogenies
My tutorials on Phylogenetic Comparative Methods
R package V.PhyloMaker2 that can generate very large phylogenies for vascular plants and R package U.PhyloMaker that can generate large phylogenetic trees for plants and animals
1.2 Source
This tutorial is publicly available and is hosted on github in the repository github.com/simjoly/ComparativeMethods-HalfDayWorkshop