Base package for phylogenetic structures and comparative data.
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.
See the help index help(package="phylobase") and run
vignette("phylobase", "phylobase") for further details and
examples about how to use phylobase.
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/)
Useful links: