Patrick Van Cleemputte
2004-Sep-01 10:25 UTC
[R] 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
Spencer Graves
2004-Sep-01 14:59 UTC
[R] lme: howto specify covariance structure between levels of grouping factors
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