User:Carl Boettiger/Notebook/Comparative Phylogenetics/2010/02/19

From OpenWetWare
Jump to: navigation, search
Owwnotebook icon.png Comparative Phylogenetics Report.pngMain project page
Resultset previous.pngPrevious entry      Next entryResultset next.png

Power in trees continues

Discussion of power in trees need a counterpoint to the example of the star tree as being devoid of information content. The best example here is probably the example tree used in the introduction of Felsenstein 1985: two star trees sharing a common ancestor. Implemented the basic creation of a balanced tree of arbitrary depth having this structure. The balanced tree has Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle 2^h -1 } nodes, all internal nodes occuring at time = 1/2 and all tips at time = 1. This sets many branch lengths to zero, which effectively turns a binary tree in an unresolved star. Setting the time of all internal nodes to zero, the age of the root, turns this into a star tree.


From the subversion log


r208 | cboettig | 2010-02-20 14:44:25 -0800 (Sat, 20 Feb 2010) | 2 lines

Implemented the creation of Felstein-style tree and a star syle tree as examples of information-rich and information-poor structure in the code felsenstein_tree.R


r207 | cboettig | 2010-02-19 11:18:01 -0800 (Fri, 19 Feb 2010) | 2 lines

removing old R code