R help - Sep 2004 - lme: howto specify covariance structure between levels of grouping factors

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

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
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html

-- 
Spencer Graves, PhD, Senior Development Engineer
O:  (408)938-4420;  mobile:  (408)655-4567