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-ph...@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. > > > ______________________________________________ R-help@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.