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RBrownie: an R package for testing hypotheses about rates of evolutionary change
Article first published online: 25 MAY 2011
DOI: 10.1111/j.2041-210X.2011.00112.x
© 2011 The Authors. Methods in Ecology and Evolution © 2011 British Ecological Society
Additional Information
How to Cite
Stack, J. C., Harmon, L. J. and O'Meara, B. (2011), RBrownie: an R package for testing hypotheses about rates of evolutionary change. Methods in Ecology and Evolution, 2: 660–662. doi: 10.1111/j.2041-210X.2011.00112.x
Publication History
- Issue published online: 5 DEC 2011
- Article first published online: 25 MAY 2011
- Received 31 December 2010; accepted 15 March 2011 Handling Editor: Robert P. Freckleton
Keywords:
- bioinformatics;
- comparative analysis;
- evolutionary biology;
- phylogenetics;
- reconstruction;
- software
Summary
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.