Re: [R-sig-phylo] Tree plotting (and maybe others) are borked when a node label is '0'

[Yan Wong]

On 4 Jan 2017, at 16:03, Emmanuel Paradis  wrote:

> This is a known feature of read.nexus(), see ape's FAQ:
> 
> http://ape-package.ird.fr/ape_faq.html#Bayestrees
> 
> This explains how to fix the problem.

Oh, sorry. I should have read the FAQ before posting. If you are thinking about 
adding a force.multi option to read.nexus, is it worth also adding a 
tip.labels.start.at.zero option to read.nexus too, and just adding that little 
code snippet right at the end of the the read.nexus code?

Yan
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Re: [R-sig-phylo] Tree plotting (and maybe others) are borked when a node label is '0'

[Emmanuel Paradis]

Hi,

This is a known feature of read.nexus(), see ape's FAQ:

http://ape-package.ird.fr/ape_faq.html#Bayestrees

This explains how to fix the problem.

Best,

Emmanuel

Le 04/01/2017 à 14:46, Yan Wong a écrit :

If I create a test.nex file as follows:

#NEXUS
BEGIN TREES;
TRANSLATE
0 0,
1 1,
2 2,
3 3,
4 4,
5 5,
6 6,
7 7;
TREE test = (((3,5),(4,6)),(0,(2,(1,7;
END;

And then attempt to do

plot(read.nexus("test.nex"))


I get
Error in plot.phylo(m) :
  tree badly conformed; cannot plot. Check the edge matrix.

It works fine if I start indexing tips at 1.

Yan

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