[R-sig-ME] incorporate pedigree into lmer
Doran, Harold
HDoran at air.org
Tue Feb 6 15:02:48 CET 2007
Well, I'm still guessing at what you want as a fixed effect and what will be random, but here is a shot
(fm1 <- lmer(weight ~ 1 +(1|Sire) + (1|Dam), data))
> -----Original Message-----
> From: Jon Hallander [mailto:Jon.Hallander at genfys.slu.se]
> Sent: Tuesday, February 06, 2007 8:26 AM
> To: Doran, Harold; r-sig-mixed-models at r-project.org
> Subject: RE: [R-sig-ME] incorporate pedigree into lmer
>
> Oh, sorry for being unclear. I am using a mixed linear model
> including both random and fixed effects:
> y = Xb + Za + e
> where the vector y are observed individual data, b is a
> vector of fixed effects, a is an individual additive random
> effect that are normally distributed vectors with
> (co)variance A*var(a). X and Z are incidence matrices
> relating the fixed and random effects (b and a) with the
> observations y. Furthermore, e is the error term, w normally
> distributed with mean zero and variance var(e). A is the
> additive genetic relationship matrix which is computed using
> the pedigree information (given below). A typical data might
> look like this:
> Id Sire Dam y (i.e. weight in kg)
> 1 Na Na 4.3
> 2 Na Na 4.7
> 3 1 2 4.4
> 4 1 Na 4.1
> 5 4 2 4.3
> 6 4 2 4.2
>
> Thanks for the help.
>
> Best regards,
> Jon
>
> -----Original Message-----
> From: r-sig-mixed-models-bounces at r-project.org
> [mailto:r-sig-mixed-models-bounces at r-project.org] On Behalf
> Of Doran, Harold
> Sent: den 6 februari 2007 13:51
> To: Jon Hallander; r-sig-mixed-models at r-project.org
> Subject: Re: [R-sig-ME] incorporate pedigree into lmer
>
> Jon
>
> I think you will find the members of this list helpful, but
> you have given zero information that we can use to help you
> with your problem. Please provide a representation of your
> model and a description of your data. Or better yet, some
> sample data. I don't have any idea what an "animal model" is
> (maybe others do), but if you can provide a statistical
> representation, maybe we can walk you through this.
>
> Harold
>
> > -----Original Message-----
> > From: r-sig-mixed-models-bounces at r-project.org
> > [mailto:r-sig-mixed-models-bounces at r-project.org] On Behalf Of Jon
> > Hallander
> > Sent: Tuesday, February 06, 2007 7:07 AM
> > To: r-sig-mixed-models at r-project.org
> > Subject: [R-sig-ME] incorporate pedigree into lmer
> >
> > 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 UMEÅ
> > 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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