[R-sig-phylo] Independent Contrasts

David Orme d.orme at imperial.ac.uk
Tue Feb 5 10:40:01 CET 2008

Hi Yorick,

The CAIC code I have written ought to cope both with calculating  
contrasts at the polytomy and matching the incomplete data to the  
tree. Randomly resolving the polytomy at the base is one option (this  
is what LDAP does in Mesquite, I think) but you then have to make a  
decision on how to downweight the resulting contrasts and possibly  
adjust the degrees of freedom.

I'd be really keen to have someone try out the code so, if you are  
having problems with it, please do let me know.


On 4 Feb 2008, at 19:36, Yorick Reyjol wrote:

> Dear all,
> I am currently trying to generate independent
> contrasts using package APE. However, I meet
> several problems which I'm not sure how to face
> and would require some help. I am not a
> phylogenetician (only an ecologist!) so may be
> some of my questions will not be appropriately formulated. Please  
> forgive me.
> 1) My phylogenetic tree has a multichotomy in its
> root. Therefore, I am not able to specify a root
> except if I discard one of the two species
> constituting the multichotomy. I have tried to
> use the function multi2di(tree, random=TRUE) to
> resolve the multichotomy and then tried to root
> my tree with function root(), but even if the
> multichotomy seems to have been resolved:
> before multi2di(): Phylogenetic tree with 191
> tips and 189 internal nodes. Unrooted
> after multi2di(): Phylogenetic tree with 191 tips
> and 190 internal nodes. Rooted.
> the function root() still generates this error message:
> Erreur dans root(tree, outgroup) :
>  the specified outgroup is not monophyletic!
> Moreover, I don't understand why my tree has
> become rooted after multi2di() was used, and
> which root was automatically chosen. Does somebody have an idea?
> 2) When I try to use the pic() function with an
> unrooted tree, some contrasts are generated, but
> numerous NaN and -Inf values are generated. As I
> believe, may this be related to the
> multichotomies I have in my tree? If yes, how is
> it possible that function multi2di() used at the
> previous step did not solve this problem?
> 3) How should I do if I want to use only a
> sub-part of my tree to generate contrasts (for
> example if I have 100 species in my dataset and
> in my tree, but only information regarding 75 of
> them for species traits). Would the use of
> drop.tip() function allow me to keep the global
> tree topology but for a subset of species?
> Many thanks for your help,
> Cheers,
> Yorick
> What should I do? Does somebody already met the same problem?
> Yorick Reyjol, Ph.D.
> Département de Chimie-Biologie
> Université du Québec à Trois-Rivières
> C.P. 500, Trois-Rivières (Québec) Canada
> G9A 5H7
> Téléphone: (819) 376-5011 poste 3379
> Télécopieur: (819) 376-5084
> http://www2.uqtr.ca/GREA/
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