[Phylobase-devl] path between two tips

[Peter Cowan]

There is a function for calculating the MRCA.  Line 101 of the  
treewalk.R file.  Perhaps this is helpful.

Peter

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:
>
> 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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>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
> ===========================================================
>
>
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