[R-sig-phylo] Independent Contrasts
Emmanuel Paradis
Emmanuel.Paradis at mpl.ird.fr
Tue Feb 5 11:18:23 CET 2008
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:
You shouldn't root() after using multi2di.
> 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?
Suppose you have a tree (A,B,C); multi2di(, random=TRUE) will generate
these three trees (with equal probability):
((A,B),C);
(A,(B,C));
((A,C),B);
All these are _rooted_ because the "root" is a node of degree 2, and so
can be considered unambiguously as such. On the other hand, the root of
the original tree is a node of degree 3.
> 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?
pic() should work only if the tree is rooted and binary (ie,
dichotomous). So I guess you missed a point here.
> 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?
Yes.
Emmanuel
> Many thanks for your help,
>
> Cheers,
>
> Yorick
>
> What should I do? Does somebody already met the same problem?
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