[Phylobase-devl] iEvoBio presentation about phylobase
hlapp at nescent.org
Wed Apr 16 23:30:45 CEST 2014
Great to see this presented at iEvoBio!
On Wed, Apr 16, 2014 at 3:56 PM, François Michonneau <
francois.michonneau at gmail.com> wrote:
> Hello all,
> I wanted to let you that I submitted an abstract for the iEvoBio
> conference (http://ievobio.org/) where I intend to give a "lightening
> talk" on phylobase. Let me know if you have any questions or feedback (I
> can edit the abstract until midnight EDT tonight).
> -- François
> phylobase: an R package for associating, manipulating and plotting
> phylogenetic trees and comparative data
> phylobase is an R package that provides S4 classes and methods to access
> and manipulate phylogenetic objects, as well as associate data to
> phylogenetic objects for comparative analysis. phylobase comes with
> methods to:
> 1. describe phylogenetic objects (e.g., number of tips and edges, is
> the tree ultrametric?);
> 2. annotate phylogenetic objects (nodes, edges and the entire object
> can be annotated);
> 3. update properties of phylogenetic objects (e.g., change edge
> 4. plot trees and associated data;
> 5. query relationships among nodes (e.g., what are the
> ancestors/descendants of a given node?);
> 6. subset phylogenetic objects (by specifying internal nodes and/or
> tips that should be included or excluded).
> The package comes with S4 classes ensuring that the data structure is
> robust, and the overhead associated with checking the validity of the
> objects is limited by using C++ code. phylobase makes use of the NCL
> library for reading NEXUS and Newick files. Over 250 unit tests are used to
> maintain the integrity and compatibility of the methods during development.
> phylobase intends to provide an intuitive, robust and efficient interface
> to complex objects, and is ideally suited to develop packages for
> phylogenetic and comparative analyses.
> Phylobase-devl mailing list
> Phylobase-devl at lists.r-forge.r-project.org
Hilmar Lapp -:- informatics.nescent.org/wiki -:- lappland.io
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