[R-sig-ME] Kinship vs. Pedigreemm

[David Duffy]

On Wed, 11 Apr 2012, Jonas Klasen wrote:

> So far as I know, in the pedigreemm package, there is only the internal 
> function pedigreemm:::ZStar which can handle covariance relationship 
> matrices. So there is no officially supported way for implementing a kinship 
> in pedigreemm,or I'm wrong?

I thought that pedigreemm(...pedigree=list()) was the official 
interface for including "the (left) Cholesky factor of the relationship 
matrix".  But yes, it sounds like it doesn't yet work with the latest 
lme4.

Cheers, David Duffy

P.S. For the curious, you can also see some code

http://genepi.qimr.edu.au/staff/davidD/Sib-pair/Src/sib-pair.R

for the LMM and probit-normal GLMM (function do_varcomp()).  It allows to 
you to add an empirical kinship matrix for VC linkage analysis.  Fitting 
is direct maximization of the likelihood using optim().  It is pretty slow 
on large kindreds (no sparse matrices etc), but a proof it is pretty easy 
to roll your own in R.  It does have the advantage of not complaining 
about non-full-rank NRMs.


-- 
| David Duffy (MBBS PhD)                                         ,-_|\
| email: davidD at qimr.edu.au  ph: INT+61+7+3362-0217 fax: -0101  /     *
| Epidemiology Unit, Queensland Institute of Medical Research   \_,-._/
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