Description

Base package for phylogenetic structures and comparative data.

Details

phylobase provides a set of functions to associate and manipulate phylogenetic information and data about the species/individuals that are in the tree.

phylobase intends to be robust, fast and efficient. We hope other people use the data structure it provides to develop new comparative methods in R.

With phylobase it is easy to ensure that all your data are represented and associated with the tips or the internal nodes of your tree. phylobase provides functions to:

• prune (subset) your trees, find ancestor(s) a descendant(s)

• find the most common recent ancestor of 2 nodes (MRCA)

• calculate the distance of a given node from the tip or between two nodes in your tree

• robust functions to import data from NEXUS and Newick files using the NEXUS Class Library (https://github.com/mtholder/ncl/)

History

phylobase was started during a Hackathlon at NESCent on December 10-14 2007.

Peter Cowan was a Google Summer of Code fellow in 2008 and developed all the code for plotting.

In December 2008, a mini-virtual Hackathlon was organized to clean up and make the code more robust.

In the spring and summer of 2009, Jim Regetz made several contributions that made the code faster (in particular with the re-ordering parts), found many bugs, and wrote most of the testing code.

phylobase was first released on CRAN on November 1st, 2009 with version 0.5.

Since then, several releases have followed adding new functionalities: better support of NEXUS files, creation of phylobase.options() function that controls the phylo4 validator, rewrite of the validator in C++.

Starting with 0.6.8, Francois Michonneau succeeds to Ben Bolker as the maintainer of the package.

More Info

See the help index help(package="phylobase") and run vignette("phylobase", "phylobase") for further details and examples about how to use phylobase.