[R-sig-phylo] basal dichotomy in phylo object

Liam J. Revell liam.revell at umb.edu
Tue Oct 25 16:55:52 CEST 2011


In my phytools package 
(http://cran.r-project.org/web/packages/phytools/index.html) there is a 
function reroot() that is really just a simple wrapper around root() 
that allows you to root along internal or terminal edges (rather than 
only at nodes).

In your example, assuming that the node 500 is tipward of 174 in the 
tree, to re-root the tree halfway along the edge leading to node number 
500 (in tree$edge), you would just do:

rooted.tree<-reroot(tree,node.number=500,position=tree$edge.length[tree$edge[,2]==500]/2)

I think.

All the best, Liam

-- 
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.revell at umb.edu
blog: http://phytools.blogspot.com

On 10/25/2011 10:44 AM, Ondřej Mikula wrote:
> Hello,
> I have an unrooted tree, but I know that basal dichotomy is between nodes
> labeled "174" and "500". I am wandering how to indicate it in the object of
> class 'phylo'. I tried 'root' function of 'ape' but with no success.
> I will be grateful for any advice. Best wishes
> Ondrej Mikula
>



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