[R-sig-ME] incorporate pedigree into lmer

[Jon Hallander]

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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