incorporate pedigree into lmer
No, The animal model requires specification of the variance-covariance matrix of the random effects, according to the pedigree (kinship) information. lmer and lmer2 currently do not allow this, as far as I know. (There is the pedigree constructor function in package lme4, as you noticed, so presumably this functionality is on the way.) You could perhaps use lme (package nlme) to fit the model, but specifying the var-covar matrix for such complex data will be painful. There is lmekin in the kinship package, which may be more useful to you. However, I haven't used it so I can't be of further help. I don't know how to estimate separate additive and dominance matrices. Maybe someone more experienced than me will reply. I think there is a need for a quantitative genetics package for R, although some qtl mapping methods seem to be implemented (See the Genetics task view on CRAN). So much statistics, so little time. *sigh* Simon.
There is Doran, Harold wrote:
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 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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Simon Blomberg, B.Sc.(Hons.), Ph.D, M.App.Stat. Centre for Resource and Environmental Studies The Australian National University Canberra ACT 0200 Australia T: +61 2 6125 7800 email: Simon.Blomberg_at_anu.edu.au F: +61 2 6125 0757 CRICOS Provider # 00120C The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. - John Tukey.