incorporate pedigree into lmer

-----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

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