[R-sig-ME] MCMCglmm and phylogeny - huge variance problem

[Jarrod Hadfield]

ccing the list

The phylogeny has internal nodes labeled, and 3 nodes are called "".  
If internal nodes are labeled, MCMCglmm is expecting them to be  
uniquely labeled.  I wonder whether this is an oversight in ape - I  
can't see why anyone would want this? Anyway...

tree$node.label<-NULL

should fix the problem.

I would drop the redundant taxa - they just add to the computing time  
unless nodes="TIPS". nodes="ALL" is preferable.

Jarrod



Quoting Szymek Drobniak <geralttee at gmail.com> on Wed, 6 Jul 2011  
21:45:05 +0200:

> Hi again,
>
> attached you'll find the data file (ref indexes studies, sp is for
> species, genus for genus - previously we've used genera instead of
> lower taxa, Zr is the response, mev is measurement error). In the sp
> column genera are merged with species names - I've noticed that ape
> removes spaces when writing tree to the file. the tree file is the one
> with branch lengths generated by compute.brlen() and it's in Newick
> format. It's a bit redundant (there are taxa not included in the
> dataset but I assumed it's not a problem as it wouldn't in cas of an
> animal model).
>
> Thanks for your help!
> Cheers,
> sz.
>
> On 6 July 2011 17:30, Jarrod Hadfield <j.hadfield at ed.ac.uk> wrote:
>> Hi,
>>
>> There definitely seems to be a problem but its hard to figure out what
>> it is. Could you attach the tree (and data)?
>>
>>
>> Jarrod
>>
>>
>> On Wed, 2011-07-06 at 17:27 +0200, Szymek Drobniak wrote:
>>> Hi,
>>>
>>> I tried compute.brlen but this works fine and computes branch lengths
>>> without any problem. I've used such trees before (without branch
>>> lengths, just topology) and they worked. Is it possible that this
>>> "duplicated levels" thing messes with everything?
>>>
>>> sz.
>>>
>>> On 6 July 2011 17:11, Jarrod Hadfield <j.hadfield at ed.ac.uk> wrote:
>>> > Hi,
>>> >
>>> > There seems to be something amiss with the tree. Do you expect there to
>>> > be branch lengths? Do you get warning messages outside of MCMCglmm if
>>> > you use compute.brlen on the phylogeny?
>>> >
>>> > Jarrod
>>> >
>>> >
>
>
> --
> Szymon Drobniak || Population Ecology Group
> Institute of Environmental Sciences, Jagiellonian University
> ul. Gronostajowa 7, 30-387 Kraków, POLAND
> tel.: +48 12 664 52 19 fax: +48 12 664 69 12
>
> www.eko.uj.edu.pl/drobniak
>



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