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Need help with Random Effect specification: nested Random Effects and a_priori known regimes (MCMCglmm)

Hi Linus,

In model 2 they are correlated, but its a bit weird. The 3x3  
covariance matrix looks like

V1   V1   V1
V1 V1+V2  V1
V1   V1  V1+V3

where V1, V2 and V3 are the variances associated with town, D2:town  
and D3:town. Amongst other things this model does not allow the  
influence of town under regimes 2 and 3 to be less than that in regime  
1.

In model 3 the effects are not correlated (because an idh structure is  
used) and the 3x3 covariance matrix looks like:

V1 0  0
0  V2 0
0  0  V3

model 1 has constant variance and perfect correlation:

V1   V1  V1
V1   V1  V1
V1   V1  V1

Perhaps better options would be

a) us(regime):town which is a completely unstructured covariance  
matrix with 6 parameters (3 variances and 3 covariances)

or

b) town+regime:town which has covariance matrix:

V1+V2  V1    V1
   V1  V1+V2  V1
   V1   V1   V1+V2

giving constant variance and constant (non-zero) correlation.

Cheers,

Jarrod

Quoting Linus Holtermann <holtermann at hwwi.org> on Mon, 24 Nov 2014  
16:21:53 +0100: