phytools: an R package for phylogenetic comparative biology (and other things)

TLDR

Let's parse. Lines: [Other] Summary 1. [Purpose] Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment. [Other] 2. [Mechanism] The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks.

Abstract

Summary 1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment. 2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks. 3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples. 4. Finally, I conclude by briefly describing an active web‐log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.