RBrownie: An R package for testing hypotheses about rates of evolutionary change

Abstract

1. Maximum likelihood analyses for testing hypotheses about how rates of disparification might vary across clades can provide important insight into the evolutionary process. While the Brownie phylogenetic library can perform such analyses, it does so outside of a general scripting environment. 2.We present RBrownie, an interface between the Brownie phylogenetic library and the R software environment, which provides easy access to the main methods in Brownie (see O'Meara 2008; PhD Dissertation, Nature Precedings), including discrete ancestral state reconstruction. In addition, RBrownie supplies a direct interface to Brownie, allowing advanced users to construct more complex combinations of analyses and to execute any newly added Brownie functions. 3.Overall, it is a package that features evolutionary rate analyses in a flexible and familiar environment. © 2011 The Authors. Methods in Ecology and Evolution © 2011 British Ecological Society.