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

Roey Angel angel at mpi-marburg.mpg.de
Mon Jun 3 18:27:13 CEST 2013

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.


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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