Re: [R] Mixed effects model with a phylogenetic tree/ distance, matrix as a random effect
Take a look at lmekin() in the coxme package. The motivating data set for my development of coxme was the Minnesota Family Breast Cancer project: 24050 subjects in 462 families. The random effect is an intercept per subject with sigma^2 K as its variance where K is the kinship matrix (1 for self-self, .5 for parent-child or sib-sib, .25 for uncle-neice, etc). lmekin is a linear models front end to the same underlying routines. I think you want lmekin(y ~ x1 + x2 + (1| subject), data=yourdata, varlist= D) or some such, where D is the similarity or "correlation" form of you distance matrix. A downside is that lmekin is sort of the poor cousin to comxe -- with finite time I've never gotton around to writing predict, residuals, plot, ... methods for it. The basic fit is fine though. Terry Therneau (In general I agree with Bert & Ben to try the other list, but I don't happen to read it.) On 06/04/2013 05:00 AM, r-help-requ...@r-project.org 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. 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 __ 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.
Re: [R] Mixed effects model with a phylogenetic tree/ distance matrix as a random effect
Bert Gunter 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 >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 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.
Re: [R] Mixed effects model with a phylogenetic tree/ distance matrix as a random effect
Recommendation: Post this to the R-sig-mixed-models list, not here. Cheers, Bert On Mon, Jun 3, 2013 at 9:27 AM, Roey Angel 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. > 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@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. > -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ 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.
