[Phylobase-devl] path between two tips

[Hilmar Lapp]

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:

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.

	-hilmar

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.
>
> Best,
> Brian
>
> 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
>> sure
>> 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
>> - ...
>>
>> Cheers,
>>
>> Thibaut.
>>
>>
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>
>
> ________________________________
> Brian O'Meara
> NESCent
> Durham, NC
> http://www.brianomeara.info
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
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