[R-sig-phylo] Functional diversity

Sebastien Lavergne sebastien.lavergne at ujf-grenoble.fr
Sun May 18 23:22:22 CEST 2008

to compute total braqnch length of a tree, you may wanna use the EH  
function of ade4 package which calculates the total evolutionary  
history of an ultrametric tree (i.e. the total sum of branch lengths)...
to do so, you'll need to use an object of class phylog (not phylo).

hope it helps

Quoting Ben Bolker <bolker at ufl.edu>:

> Yorick.Reyjol at UQTR.CA wrote:
>>   Dear community members,
>>   I am trying to calculate a functional diversity index, following   
>>  recommendations by Petchey & Gaston (2002). Functional Diversity   
>> (FD), species richness and community composition.  /Ecology letters  
>>  /5:  402-411. This requires calculating the total branch length of  
>>  a tree  obtained by hierarchical clustering on a species traits   
>> matrix. Is it  possible to calculate a total branch length   
>> (including internal  branches) using APE? I already know the   
>> argument  "name.tree$edge.length" but it only gives the individual   
>> length of  final tree branches.
>>   Many thanks for your help,
>>   Yorick
>  I think you're looking for cophenetic.phylo() or dist.nodes() .  (I
> must admit that even though I knew
> that such a function existed, I had to spend a while looking for it ...
> I wonder if there's
> some kind of "alias" entry that would make this easier to find?)
>  Ben Bolker
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  Sebastien Lavergne
  Laboratoire d'Ecologie Alpine, UMR-CNRS 5553
  Universite Joseph Fourier
  BP 53, 38041 Grenoble Cedex 9, France
  tel +33 (0)4 76 63 54 50
  fax +33 (0)4 76 51 42 79

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