[R-sig-phylo] similarity of trees

Emmanuel Paradis emmanuel.paradis at ird.fr
Wed Jan 19 04:18:12 CET 2011


Hi Damien & Scott,

I don't know the formula of Icong or MAST, but I'd like to remind you 
the function prop.part() that finds all the clades in a set of trees 
and returns the compositions and frequencies, eg:

> a <- rtree(4)
> b <- rtree(4)
> prop.part(c(a, b))
1: t2
2: t1
3: t3
4: t4

==> 2 time(s):[1] 1 2 3 4
==> 1 time(s):[1] 2 3 4
==> 2 time(s):[1] 2 3
==> 1 time(s):[1] 1 2 3

This requires the trees to have the same tip labels. It is used in ape 
by boot.phylo(), and calls a C code. It doesn't seem to be used by 
other developers though it is certainly efficient and may help in many 
applications.

Emmanuel

On Tue, 18 Jan 2011 19:46:30 +0100 "Damien de Vienne" 
<damien.de-vienne at u-psud.fr> wrote:
> 
> Dear Scott, 
> Having Icong in R would be nice but it is not the case
> yet. Sorry...
> 
> However if someone has a code (in C for
> example) to compute the maximum  agreement subtree (MAST) between 
>two
> trees, I would be happy to do the  rest in order to have the Icong 
>index
> within R (within the ape package maybe ? And having the simple MAST
> calculation there would be also very useful I believe). 
> 
> 
> Anyway, if you want to automate the calculation of the Icong index 
>you 
> can still use PAUP* that calculates the MAST and apply afterwards 
>the 
> functions that are in the paper. 
> If you need help, tell me. 
> 
> Damien
> 
> 
> 
> Le Mar 18 janvier 2011 19:42, Scott
> Chamberlain a ?crit :
>> Hi Marten,
>> 
>> 
>> 
>> The test I referred to tests for similarity of topology
> only, ignoring
>> branch lengths. On the website made by de Vienne
> et al. you can input two
>> newick trees and the site calculates
> the Icong index, which determines
>> how similar the topologies
> are, and gives you a p-value. I use it in the
>> context of trying
> to argue that a tree I have made is *similar enough* to
>> a
> published tree of the same group of organisms. I believe you have to
>> delete all unshared taxa between the two trees you input.
>>
> 
>> 
>> I am interested purely in the trees, not community
> ecology data, so
>> phylosor and NRI are not applicable in this
> case.
>> 
>> 
>> Scott
>> On Tuesday, January
> 18, 2011 at 12:34 PM, Marten Winter wrote:
>> 
>> 
>>> Dear Scott,
>>> 
>>> 
>>> do you
> really want to test for similarity of the shape of the trees? If
>>> yes please let me know how to do this :O)
>>> 
>>> If you would also be satisfied with a similarity based on the
> shared
>>> branches I suggest something like Phylosor or may be
> NRI...
>>> 
>>> cheers, Marten
>>> 
>>> 
>>> 
>> 
>> 
>> 
>> 
>> 
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>> 
>> 
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>>
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