Hi Yan,

it seems we introduced a small bug with making these functions generic.
Replace in the function .multi2di_ape the line
phy <- reorder(phy)
with
phy <- .reorder_ape(phy, "cladewise", FALSE, n, 1L)
and it should work. You have to recompile ape afterwards.

Cheers,
Klaus





On Fri, Jan 13, 2017 at 1:24 PM, Yan Wong <y...@yanwong.me> wrote:

> Thanks. I think that’s because read_nexus_phylo() doesn’t do
> .compressTipLabel automatically
>
> n <- read_nexus_phylo("tmp.nex")
> n2 <- .compressTipLabel(n)
> multi2di(n2) #this causes an error.
>
> Unfortunately I need the .compressTipLabel functionality really.
>
> Yan
>
>
> On 13 Jan 2017, at 17:06, François Michonneau <
> francois.michonn...@gmail.com> wrote:
>
> > Hi Yan,
> >
> >  I'm not sure about what's going on here, but it works with the rncl
> > package (http://cran.r-project.org/web/packages/rncl/index.html)
> >
> >  install.packages("rncl")
> >  library(rncl)
> >  n <- read_nexus_phylo("tmp.nex")
>
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>



-- 
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/

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