[R] Mixed effects model with a phylogenetic tree/ distance matrix as a random effect

[Ben Bolker]

Bert Gunter <gunter.berton <at> gene.com> writes:

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

  Seconded.  Alternatively you could try the r-sig-phylo at r-project.org
mailing list, although I think I would try R-s-m-m first.

> 
> 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.

  This is not going to change in the near future, although
there is a 'pedigreemm' package built on lme4 that 
might do what you want.

  You might be able to use MASS::glmmPQL in conjunction with
the corStruct structures from nlme (for classical geostatistical
correlation models); ape (for phylogenetic models); or ramps (other
choices).

  INLA might ??? allow tree correlation structures:
http://arxiv.org/abs/1210.4908

  Ives and Garland have some MATLAB code for phylogenetic 
logistic regression ...

> > 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
> >
> >
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> >
>