[R-sig-ME] incorporate pedigree into lmer

[Doran, Harold]

It's good to keep this on list for others to chime in and for reference. You need the ranef extractor

ranef(fm1)$sire 

> -----Original Message-----
> From: Jon Hallander [mailto:Jon.Hallander at genfys.slu.se] 
> Sent: Tuesday, February 06, 2007 10:41 AM
> To: Doran, Harold
> Subject: RE: [R-sig-ME] incorporate pedigree into lmer
> 
> Ok, thanks! This seems to work, but does it utilize the 
> pedigree information? When I type the command summary(fm1) I 
> do not get individual random effect values (breeding values), 
> but variances of the random effects:
> 
> > fm1 <- lmer(y ~ 1 +(1|sire) + (1|dam), data)
> > summary(fm1)
> Linear mixed-effects model fit by REML
> Formula: y ~ 1 + (1 | sire) + (1 | dam) 
>    Data: data1 
>    AIC   BIC logLik MLdeviance REMLdeviance
>  28.24 27.62 -11.12      23.45        22.24
> Random effects:
>  Groups   Name        Variance Std.Dev.  
>  sire     (Intercept) 1.75e-09 4.1833e-05
>  dam      (Intercept) 1.75e-09 4.1833e-05
>  Residual             3.50e+00 1.8708e+00
> number of obs: 6, groups: sire, 4; dam, 3
> 
> Fixed effects:
>             Estimate Std. Error t value
> (Intercept)   3.5000     0.7638   4.583
> 
> 
> 
> /Jon
> 
> -----Original Message-----
> From: Doran, Harold [mailto:HDoran at air.org]
> Sent: den 6 februari 2007 15:03
> To: Jon Hallander; r-sig-mixed-models at r-project.org
> Subject: RE: [R-sig-ME] incorporate pedigree into lmer
> 
> 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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