[Phylobase-devl] path between two tips

Ben Bolker bolker at ufl.edu
Thu Nov 20 21:02:54 CET 2008

Thibaut Jombart wrote:
> Hilmar Lapp wrote:
>> Yep pretty much what I would have said. If there isn't already, why 
>> not just have a shortestPath method that takes any two nodes?
> My bad. The algorithm is the same, but I just needed it for two tips. Ok 
> for 'shortestPath'.
>> BTW another thought, as trees are graphs, it's also a possibility to 
>> have an easy conversion to a graph data structure and then have all 
>> the methods at hand supported on that data structure. For example, 
>> there is the graph package on CRAN:
>> http://cran.stat.ucla.edu/web/packages/graph/index.html
>> and a whole variety of algorithms on that data structure in the RBGL 
>> package:
>> http://cran.stat.ucla.edu/web/packages/RBGL/index.html
>> including several for shortest path.
> Yes, but maybe that would be overkill. I mean, calling from a graph 
> package would be more powerful, but I have no idea how many of these 
> newly accessible tools would be useful for phylogeny.
> Best,
> Thibaut.

  It's a nice idea in general, and in keeping with idea of phylobase
as a "glue" package that makes available methods from many different
places (ape, geiger, ouch, ade4 as well as RBGL etc etc etc) ... but
since you already have an answer to this one it's certainly unnecessary ...


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