[Phylobase-devl] path between two tips
pdc at berkeley.edu
Thu Nov 20 20:28:17 CET 2008
There is a function for calculating the MRCA. Line 101 of the
treewalk.R file. Perhaps this is helpful.
On Nov 20, 2008, at 10:54 AM, 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?
> 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:
> and a whole variety of algorithms on that data structure in the RBGL
> including several for shortest path.
> On Nov 20, 2008, at 1:34 PM, Brian O'Meara wrote:
>> Two thoughts:
>> Why not make it a little more general and return the nodes on the
>> shortest path between any two nodes? ("nodes" in the general tree
>> sense of nodes, both internal nodes and tips, not as a synonym for
>> internal nodes). I would guess that this wouldn't add much complexity
>> if you're doing something like finding the MRCA for two nodes and
>> recording the nodes between the MRCA and each of the chosen
>> descendants (reversing the order of the nodes returned for one
>> descendant, and including the MRCA).
>> I'd avoid the path2tips name as there are a lot of functions (in
>> other packages) that use a2b to refer to converting an object of type
>> "a" to an object of type "b".
>> I don't know for certain that such a function isn't in phylobase
>> already, btw.
>> On Nov 20, 2008, at 1:21 PM, Thibaut Jombart wrote:
>>> Hi again,
>>> here is another proposition of function. In fact, I would just make
>>> that it does not already exist somewhere before commiting. I wrote a
>>> function finding all the nodes on the shortest path from one tip to
>>> another. It could be part of the treewalk stuff.
>>> My deepest problem now is with the function's name (advice welcome):
>>> - path2tips
>>> - tipsPath
>>> - pathTips
>>> - shortestPathBetweenTwoTips
>>> - ...
>>> Phylobase-devl mailing list
>>> Phylobase-devl at lists.r-forge.r-project.org
>> Brian O'Meara
>> Durham, NC
>> Phylobase-devl mailing list
>> Phylobase-devl at lists.r-forge.r-project.org
> : Hilmar Lapp -:- Durham, NC -:- hlapp at duke dot edu :
> Phylobase-devl mailing list
> Phylobase-devl at lists.r-forge.r-project.org
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