Rooting trees using ape

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Rooting trees using ape

Chris Jones-35
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,
Chris

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Re: Rooting trees using ape

Ben Bolker

Chris Jones-35 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:

[snip]
  Can you post your dataset, or a subset of it that replicates
the problem, somewhere?  (On the list if short, otherwise
on some web site somewhere.)   [See "reproducible
example" in the posting guide.]

  cheers
    Ben Bolker
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Re: Rooting trees using ape

Simon Blomberg-4
In reply to this post by Chris Jones-35
Please supply enough information to allow us to reproduce the error.
Also, nirK.tree is a different object to nirk.tree, which might be
confusing things.

Simon.

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,
> Chris
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> 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
Australia
Room 320 Goddard Building (8)
T: +61 7 3365 2506
email: S.Blomberg1_at_uq.edu.au

Policies:
1.  I will NOT analyse your data for you.
2.  Your deadline is your problem.

The combination of some data and an aching desire for
an answer does not ensure that a reasonable answer can
be extracted from a given body of data. - John Tukey.

______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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