Re: [R-sig-phylo] Rooting a tree with a basal polytomy

2017-02-07 Thread Yan Wong 
Perfect, thanks.

Yan

On 7 Feb 2017, at 13:40, Emmanuel Paradis  wrote:

> Hi,
> 
> If you have a single tree (object of class "phylo")
> 
> phy$root.edge <- 0
> 
> If there are several trees in your NEXUS file (then phy is of class 
> "multiPhylo"):
> 
> for (i in seq_along(phy)) phy[[i]]$root.edge <- 0

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Re: [R-sig-phylo] Rooting a tree with a basal polytomy

2017-02-07 Thread Emmanuel Paradis 

Hi,

If you have a single tree (object of class "phylo")

phy$root.edge <- 0

If there are several trees in your NEXUS file (then phy is of class 
"multiPhylo"):


for (i in seq_along(phy)) phy[[i]]$root.edge <- 0

Best,

Emmanuel

Le 07/02/2017 à 13:17, Yan Wong a écrit :

Sorry if this is a trivial question, but I have some (rooted) nexus trees with 
polytomies at the root. When I read them in using read.nexus() they are treated 
as unrooted. What’s the easiest way to tell R that they are intended to be 
rooted, even though the root is a polytomy? There’s no ‘force.rooted’ option to 
any of the tree reading routines that I can see.

Cheers

yan
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