[R-sig-phylo] randomizing clades within a node

Emmanuel Paradis Emmanuel.Paradis at ird.fr
Thu Jan 19 02:55:04 CET 2012


Hi Juan,

Juan Antonio Balbuena wrote on 13/01/2012 21:57:
>   Hello
>
> I would very much appreciate if someone can help me with this one. I
> wish to compare two additive trees that are identical for some but not
> all the clades.
>
> So I use rtree of the ape package with, say, 10 tips to generate tree
> "A". Then I wish to modify "A" to get tree "B" by randomizing the clades
> and patristic distances in a given number of nodes. If the number of
> nodes is, for instance, three, the 3 nodes furthest apart from the
> origin will be randomized. Then "A" and "B" will be compared. The whole
> procedure needs to be carried out a large number of times (10,000).

The functions you need are extract.clade and bind.tree. The both have 
options to allow you to flexibly handle eventual root edges, so have a 
look at their help pages.

HTH

Emmanuel

> Any help would be much appreciated.
>
> Juan A. Balbuena
>
> --
> Dr. Juan A. Balbuena
> Marine Zoology Unit
> Cavanilles Institute of Biodiversity and Evolutionary Biology
> University of Valencia http://www.uv.es/~balbuena
> <http://www.uv.es/%7Ebalbuena>
> P.O. Box 22085 http://www.uv.es/cavanilles/zoomarin/index.htm
> 46071 Valencia, Spain http://cetus.uv.es/mullpardb/index.html
> e-mail: j.a.balbuena at uv.es <mailto:j.a.balbuena at uv.es> tel. +34 963 543
> 658 fax +34 963 543 733
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> NOTE! For shipments by EXPRESS COURIER use the following street address:
> C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain.
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
> _______________________________________________
> R-sig-phylo mailing list
> R-sig-phylo at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

-- 
Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/



More information about the R-sig-phylo mailing list