R help - Jun 2013 - 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-request at 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