R help - Jun 2013 - Mixed effects model with a phylogenetic tree/ distance matrix as a random effect

Hi,
I'm trying to build a mixed-effects model in which I'd like to include 
either a distance matrix or a phylogenetic tree as a random effect.
The troubles I've had are that:
1. Function lmer() in package lme4 only accepts a data frame column as a 
random factor and not a distance matrix.
2. Function MCMCglmm() in package MCMCglmm only accepts a rooted and 
ultrametric phylogenetic tree as a pedigree argument while my tree is 
neither (and for various reasons I cannot construct one or coerce mine 
to be a rooted, ultrametric tree).

Is there any way around it?
I'd appreciate mostly a solution to problem 1.

Roey

-- 
Dr. Roey Angel

Max-Planck-Institute for Terrestrial Microbiology
Karl-von-Frisch-Strasse 10
D-35043 Marburg, Germany

Office: +49 (0)6421/178-832
Mobile: +49 (0)176/612-785-88

Recommendation: Post this to the R-sig-mixed-models  list, not here.

Cheers,
Bert

On Mon, Jun 3, 2013 at 9:27 AM, Roey Angel <angel at mpi-marburg.mpg.de>
wrote:
> Hi,
> I'm trying to build a mixed-effects model in which I'd like to
include
> either a distance matrix or a phylogenetic tree as a random effect.
> The troubles I've had are that:
> 1. Function lmer() in package lme4 only accepts a data frame column as a
> random factor and not a distance matrix.
> 2. Function MCMCglmm() in package MCMCglmm only accepts a rooted and
> ultrametric phylogenetic tree as a pedigree argument while my tree is
> neither (and for various reasons I cannot construct one or coerce mine to
be
> a rooted, ultrametric tree).
>
> Is there any way around it?
> I'd appreciate mostly a solution to problem 1.
>
> Roey
>
> --
> Dr. Roey Angel
>
> Max-Planck-Institute for Terrestrial Microbiology
> Karl-von-Frisch-Strasse 10
> D-35043 Marburg, Germany
>
> Office: +49 (0)6421/178-832
> Mobile: +49 (0)176/612-785-88
>
>
> ______________________________________________
> R-help at r-project.org 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.
>


-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm