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incorporate pedigree into lmer

2 messages · Jon Hallander, David Duffy

Original
Jon Hallander
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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.

Best regards,
Jon Hallander

____________________________________________

Jon Hallander
Department of Forest Genetics and Plant Physiology
Swedish University of Agricultural Sciences
SE-901 83 UME?
SWEDEN
Phone: +46 90 786 82 80
Mobile: +46 70 220 08 79
Fax: +46 90 786 81 65
E-mail: jon.hallander at genfys.slu.se
____________________________________________
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David Duffy
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On Tue, 6 Feb 2007, Jon Hallander wrote:

            

      
      
      
    

        
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.