Introduction.- First Steps in R for Phylogeneticists.- Phylogenetic Data in R.- Plotting Phylogenies.- Phylogeny Estimation.- Analysis of Macroevolution with Phylogenies.- Simulating Phylogenies and Evolutionary Data.- Developing and Implementing Phylogenetic Methods in R.- Short Course on Regular Expressions.
This is great - demystifying phylogenetic analysis using all those packages in R. So far, I've only got as far as staring at a pretty primate tree, but I'm going to do great things!
This book is about an R package, and yet is also about phylogenetic analyses and how to do them sensibly. It is digestible and readable and understandable... which is VERY unusual for R help.