Mixed effects model with a phylogenetic tree/ distance matrix as a random effect
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
______________________________________________ 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.