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 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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