[R-sig-ME] incorporate pedigree into lmer

[Doran, Harold]

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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