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Message-ID: <00e101d09240$3a55ad00$af010700$@gmail.com>
Date: 2015-05-19T14:29:33Z
From: Alexandre Martin
Subject: genetic effects and multiple membership in MCMCglmm (Alexandre Martin)
In-Reply-To: <CANXb-o5zZBsrPa_6OmQhJcgLQpSxggydTeMhEcGKMFYhsRSWNQ@mail.gmail.com>

Hi Szymek, 

 

Thank you very much for your excellent answer that allowed me to understand
a couple of things in MCMCglmm. 

Thanks again.

 

Alexandre

 

De : Szymek Drobniak [mailto:szymek.drobniak at uj.edu.pl] 
Envoy? : 14 mai 2015 17:39
? : r-sig-mixed-models at r-project.org
Cc : alexandre.m.martin at gmail.com
Objet : Re: genetic effects and multiple membership in MCMCglmm (Alexandre
Martin)

 

Hello Alexandre,

 

using ped assigns a given correlation structure only to the "animal" random
effect. You have to create an inverse of A matrix:

 

my_inverse <- inverseA(ped)$Ainv

 

and assign it in MCMCglmm to specific random effects:

 

MCMCglmm(Y~1,
random=~animal+mm(m1+m2+m3),

ginverse=list(animal=my_inverse, m1=my_inverse,
m2=my_inverse,m3=my_inverse), data=dat, pr=T).

 

Cheers

Szymek


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