[R] Mixed effects model with a phylogenetic tree/ distance matrix as a random effect
gunter.berton at gene.com
Mon Jun 3 20:35:29 CEST 2013
Recommendation: Post this to the R-sig-mixed-models list, not here.
On Mon, Jun 3, 2013 at 9:27 AM, Roey Angel <angel at mpi-marburg.mpg.de> wrote:
> 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
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> and provide commented, minimal, self-contained, reproducible code.
Genentech Nonclinical Biostatistics
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