[R] Rooting trees using ape
s.blomberg1 at uq.edu.au
Thu Oct 11 02:17:37 CEST 2007
Please supply enough information to allow us to reproduce the error.
Also, nirK.tree is a different object to nirk.tree, which might be
On Wed, 2007-10-10 at 15:07 +0200, Chris Jones wrote:
> Hi all,
> I seem to be having a difficult time using the 'ape' package in R
> when it comes to rooting trees. Here's a short screenshot:
> > nirK.tree
> Phylogenetic tree with 23 tips and 21 internal nodes.
> Tip labels:
> Burkholder, Burkholde3, Burkholde1, Burkholde4, Burkholde5,
> Ralstonia2, ...
> Node labels:
> , 100, 100, 100, 70, 91,...
> Unooted; includes branch lengths.
> > test<-root(nirk.tree, 4)
> Error in root(nirk.tree, 4) : subscript out of bounds
> > test<-root(nirk.tree, "Burkholde4")
> Error in root(nirk.tree, "Burkholde4") : subscript out of bounds
> I tried with the example tree provided in the package, and that
> seemed to work ok. Any suggestions?
> Many thanks,
> R-help at r-project.org mailing list
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
Simon Blomberg, BSc (Hons), PhD, MAppStat.
Lecturer and Consultant Statistician
Faculty of Biological and Chemical Sciences
The University of Queensland
St. Lucia Queensland 4072
Room 320 Goddard Building (8)
T: +61 7 3365 2506
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