[R] Adding correlation and or variance structure in mixed models

Laz lmramba at ufl.edu
Mon Apr 7 18:12:54 CEST 2014

Dear R users,

I am using mixed models to analyze genetic experiments. I have tried to 
use R packages such as lme4, nlme. I am looking for a model that can 
allow me to specify my correlation structure and the same time allow to 
have more than 2 random effects in the model. None of the above packages 
fully answer  my question and some results obtained have incorrect  
degrees of freedom at some point.

For example: Y = XB + Z1g + Z2f + e
where X is the design matrix of fixed effect, B is the vector of fixed 
effect, Z1 is a random design matrix of the first random variable,g,  
and g is the vector of the random effect g, Z2 is random design matrix 
of the second random variable,  and f is a vector of the random effect 
f., e is the residual error.
If I need to specify an autocorrelation structure such as AR1 
(autocorrelation 1st order) or CORG (general correlation) how would I do 
that in R? the functions provided do not allow to specify this term 
except the gls but it does not take random effects.

I am interested in specifying variance structures such as AR1V 
(autocorrelation 1st order), diagonal, uniform heterogeneous, uniform 
correlation, Unstrustured etc in my model that has both fixed and 
several random effects. Which R packages or functions will help me to 
accomplish this?


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