My suggestion below should work with trees initially with zero-length branch if
using a negative value instead of 0, e.g.:
tr$edge.length[j] <- -1
Then di2multi(tr, tol = -0.5)
Emmanuel
-----Original Message-----
From: "Emmanuel Paradis" <emmanuel.para...@ird.fr>
Sender: r-sig-phylo-boun...@r-project.org
Date: Wed, 28 Sep 2011 14:10:55
To: Daniel Rafael Miranda-Esquivel<dmira...@uis.edu.co>;
<r-sig-phylo-boun...@r-project.org>; <r-sig-phylo@r-project.org>
Reply-To: emmanuel.para...@ird.fr
Subject: Re: [R-sig-phylo] Collapsing nodes using node.labels
Hello Daniel,
Try this small manipulation ('tr' is your tree and 'node' stores the label of
the node):
i <- which(tr$node.label == node)
j <- which(tr$edge[, 2] == i + Ntip(tr))
tr$edge.length[j] <- 0
Then di2multi(tr) will do the job. (Hopefully, there's originally no
zero-length branch in tr.)
HTH
Emmanuel
-----Original Message-----
From: Daniel Rafael Miranda-Esquivel <dmira...@uis.edu.co>
Sender: r-sig-phylo-boun...@r-project.org
Date: Wed, 28 Sep 2011 00:21:43
To: <r-sig-phylo@r-project.org>
Subject: [R-sig-phylo] Collapsing nodes using node.labels
Hello all,
I am trying to collapse some nodes in a tree but using node.label and
not edge.length, is there a way to convert node.label to
edge.length? or a function to collapse a node but using node.label
directly?
Daniel
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