[R-sig-ME] incorporate pedigree into lmer

David Duffy David.Duffy at qimr.edu.au
Tue Feb 6 23:19:11 CET 2007

On Tue, 6 Feb 2007, Jon Hallander wrote:

> Hello,
> I am a novice using the lme4 library and would like some help regarding 
> the function lmer. I would like to solve the animal model using several 
> random effects (e.g. individual (animal) and dominance effects). Also, I 
> would like to infer the additive and dominance relationship matrices 
> (covariance matrices). The function pedigree can set up the pedigree 
> structure, but how do I use it in the lmer function? I have not found 
> any convenient example. Thanks in advance.

It is not yet possible to fit biometrical genetic type models in lmer. 
You can use the kinship package (which calls lme), but that can be slow 
for big animal breeding type datasets.  I haven't done timings on some of 
the other R mixed model packages such as lmm.

Have you tried Wombat? That's Karin Meyer's successor for DFREML.  In one 
comparison I did, it took 3 seconds where kinship's lmekin took over an 
hour ;) See http://agbu.une.edu.au/kmeyer/wombat.html.  If you are 
specifically interested in generalized linear mixed models eg binomial, 
then your best bet currently, I think, is to write the model in BUGS.

David Duffy.

| 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   \_,-._/
| 300 Herston Rd, Brisbane, Queensland 4029, Australia  GPG 4D0B994A v

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