[R] lme: howto specify covariance structure between levels of grouping factors

Spencer Graves spencer.graves at pdf.com
Wed Sep 1 16:59:03 CEST 2004

      1.  Have you followed "the posting guide! 
http://www.R-project.org/posting-guide.html"?  In many cases, it might 
help you answer your own questions.  If not, it might help you formulate 
a question in a way that might generate more useful replies. 

      2.  Have you studied Pinhiero and  Bates (2000) Mixed Effects 
Models in S and S-Plus (Springer)?  In my opinion, this is an excellent 
book on the subject, and I was not able to use lme effectively until 
after I had studied that book. 

      hope this helps.  spencer graves

Patrick Van Cleemputte wrote:

> Dear all,
> I am studying the possibility of using the nlme package in R to 
> analyse field trials of agricultural crops. I have a problem with the 
> syntax for the modelling of variance covariance structures. I can 
> model the within-group covariance structure using the correlation 
> argument and the covariance structure between different random effects 
> of the same grouping level using 'random=pdDiag(~effect)|group' but I 
> would like to model the covariance structure' between' the different 
> levels of the grouping factor. This is necessary because the plants (= 
> grouping factor) we are testing are not independant. They are 
> genetically correlated and usually we know this correlation. I would 
> therefore also like to specify the exact (not starting) values of this 
> 'between subjects correlation'.
> Can you tell me if this is possible in R and how the syntax of such a 
> model would look like?
> thank you in advance,
> P.
> http://entertainment.msn.be/muziek/musicclub
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Spencer Graves, PhD, Senior Development Engineer
O:  (408)938-4420;  mobile:  (408)655-4567

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