From francois.michonneau at gmail.com Wed Apr 16 21:56:10 2014 From: francois.michonneau at gmail.com (=?UTF-8?Q?Fran=C3=A7ois_Michonneau?=) Date: Wed, 16 Apr 2014 15:56:10 -0400 Subject: [Phylobase-devl] iEvoBio presentation about phylobase Message-ID: 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). cheers, -- Fran?ois *Title* phylobase: an R package for associating, manipulating and plotting phylogenetic trees and comparative data *Abstract* 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 lengths); 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From hlapp at nescent.org Wed Apr 16 23:30:45 2014 From: hlapp at nescent.org (Hilmar Lapp) Date: Wed, 16 Apr 2014 17:30:45 -0400 Subject: [Phylobase-devl] iEvoBio presentation about phylobase In-Reply-To: References: Message-ID: Great to see this presented at iEvoBio! -hilmar On Wed, Apr 16, 2014 at 3:56 PM, Fran?ois 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). > > cheers, > -- Fran?ois > > > *Title* > > phylobase: an R package for associating, manipulating and plotting > phylogenetic trees and comparative data > > *Abstract* > > 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 > lengths); > 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 > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-devl > -- Hilmar Lapp -:- informatics.nescent.org/wiki -:- lappland.io -------------- next part -------------- An HTML attachment was scrubbed... URL: