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RBrownie: an R package for testing hypotheses about rates of evolutionary change
Author(s) -
Stack J. Conrad,
Harmon Luke J.,
O'Meara Brian
Publication year - 2011
Publication title -
methods in ecology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.425
H-Index - 105
ISSN - 2041-210X
DOI - 10.1111/j.2041-210x.2011.00112.x
Subject(s) - r package , computer science , phylogenetic tree , scripting language , interface (matter) , clade , software package , process (computing) , software , biology , operating system , computational science , biochemistry , bubble , maximum bubble pressure method , gene
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.