From: William Valdar <valdar_at_well.ox.ac.uk>

Date: Wed 18 May 2005 - 00:22:07 EST

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Wed May 18 00:40:53 2005

Date: Wed 18 May 2005 - 00:22:07 EST

Hi,

> I'm afraid that I don't understand what you are trying to do. With a

*> formula of ~ 1 the pdSymm generator creates a 1x1 variance-covariance
**> matrix, which you are initializing to a 3x3 matrix.
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Oh... I had a feeling I was doing something wrong there.

> What is batch.mat supposed to represent?

I would like to use batch.mat to specify a correlation structure for the batches A, B and C. Specifically, I wish to work out the contribution to the variance of the batch random effect, given that I know some pairs of batches (eg, A and B) are going to be more similar than other pairs (eg, A and C) and how similar they are likely to be. My (mis?)reading of P&B p165 suggested this may be possible turning some of the pdIdents into pdSymms.

I was hoping to use this test example as a prelude to using genetic relationship data to impose a correlation structure on a subject-level or family-level effect. I understand from an earlier post (Jarrod Hadfield, 2003) that lme is not really optimized for this, but I would nontheless like to evaluate to what extent it can do it anyway. The example used in that post was extreme: each case was effectively a different realization of a random effect where the correlation between levels is known. My needs are simpler: in the example I gave above, batches A, B and C might represent three families related by different degrees.

> Yes, although I think you mean lmer in lme4. Because the lmer function

*> allows multiple nested or non-nested grouping factors, the need for the
**> pdMat classes is eliminated (or greatly reduced) and the code can be
**> simplified considerably. There is an article in the 2005/1 issue of R
**> News describing the use of lmer.
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Thanks for pointing this out as I had missed this article. I know lmer is under development and am very interested in what it can do. Having found lme/lmer useful for more standard problems I would like to use it for genetic-type analysis where possible rather than resort to a different language (eg SAS) or specialized proprietary software (eg, ASREML). However, I understand that may not be possible.

William

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Dr William Valdar ++44 (0)1865 287 717 Wellcome Trust Centre valdar@well.ox.ac.uk for Human Genetics, Oxford www.well.ox.ac.uk/~valdar ______________________________________________R-help@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 Received on Wed May 18 00:40:53 2005

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