[R-sig-ME] design matrices in MCMCglmm

Alexandre Martin alexandre.m.martin at gmail.com
Fri Mar 27 21:39:40 CET 2015

Dear all,

I am working on estimating maternal effects (genetic and environmental) 
with MCMCglmm that is new for me.

I am trying to apply to MCMCglmm what is shown in online Muir's course 
notes made for SAS. Leanning on Henderson’s Mixed Model Equation, these 
notes explain how to solve MME to predict random effects “by hand”.

Here is my concern:

I do not know how to extract the design matrices for a MCMCglmm model, 
e.g. the relatedness matrix or the one for maternal genetic effects. I 
want that to understand how the design matrices are constructed by 
comparing them to what they are supposed to look like.  For instance, 
the design matrix for maternal genetic effects should relate offspring 
to all the individuals that are in the pedigree, whereas the design 
matrix for maternal environmental effects should just relate offspring 
to their mothers. Does such a difference exist when MCMCglmm constructs 
its design matrices? If not, how to include such different matrices in 

Any help will be greatly appreciated. Thank you!


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