[R-sig-ME] Split-plot Design
Andrew Robinson
A.Robinson at ms.unimelb.edu.au
Sun Mar 23 23:09:43 CET 2008
Hi Ribeiro,
try section 1.6 of Pinheiro and Bates, as a starting point, and/or
section 10.2 of Venables and Ripley.
Andrew
On Sun, Mar 23, 2008 at 06:15:21PM -0300, marcioestat at pop.com.br wrote:
>
>
>
> Hey
> listers,
>
> ?
>
>
>
> ?
>
> It’s good to know that I still
> have a lot of search to do…
>
> ?
>
> According to the two procedures AOV
> and LME, I got two different results and I didn’t understand at all
> the results of LME… There is a coefficient estimate of each level
> and I just pretend to test if the effects of the factors and interaction
> are significant or not…So I would like to learn more about this
> function, because it's adequate for split-plot design...
> test.anova=
> aov(mes ~ nitro*thatch + Error(block/nitro), data=test)
>
> ?
>
> summary(test.anova)
>
> ?
>
> test.lme
> <- lme(mes ~ nitro*thatch,random= ~ 1|block/nitro, data=test)
>
> ?
>
> summary(test.lme)
>
> ?
>
> Does anybody has any document or
> reference that explain this results in details of the lme…
> I’ve looked for, but I didn’t find any good
> explication… I notice that there is a lot of information about the
> lmer, but I am going step by step…
>
> ?
>
>
>
> ?
>
> Thanks,
>
> ?
>
>
>
> ?
>
> Ribeiro
>
> ?
>
>
> ?
> > Thanks for your response John. I just have one quick comment
> about
> > the Kenward-Roger degrees of freedom calculation. It has
> been some
> > time since I looked at that paper but my impression
> at the time was
> > that the equations would not easily translate
> into the formulation
> > used in lmer. The approach used in lmer is
> like that of Henderson's
> > mixed model equations (with many
> modifications). That is, it is based
> > on a penalized least
> squares problem, not a generalized least squares
> > problem. My
> recollection is that Kenward and Roger wrote their
> > equations in
> terms of the generalized least squares problem.
> >
> > You
> are not the first person to suggest that incorporating the
> >
> Kenward-Roger calculation would enhance lmer. The reason I haven't
> > done so is that I believe it is far from trivial to do so and I
> have
> > many, many other enhancements I would prefer to spend my
> time on.
> > However, this is open source software and any
> enterprising person who
> > wants to implement it is more than
> welcome to do so. It may be
> > sufficiently involved to be a
> thesis topic - I don't know because I
> > haven't studied it
> carefully enough.
> >
> > Any person considering doing that
> should read or reread Bill Venables'
> > "Exegeses on Linear
> Models" before embarking on it. As he points out
> > in his
> discussion of modifications made in S-PLUS to emulate some
> >
> calculations in SAS, the "brute force" approach of taking a set
> of
> > equations and implementing them literally is rarely a good
> approach.
> > So I am not talking about a "pidgin R"
> implementation here where a
> > linear least squares calculation is
> written
> >
> > XpX <- t(X) %*% X
> > XpXinv <-
> solve(XpX)
> > Xpy <- t(X) %*% y
> > betahat <- XpXinv
> %*% Xpy
> >
> > An mer object includes slots L, RZX and RX
> that define the Cholesky
> > decomposition of the crossproduct
> matrix that is more-or-less like
> > that in the Henderson mixed
> model equations. The L slot itself has a
> > Perm slot that gives
> the fill-reducing permutation P for the random
> > effects. That
> may not be relevant - I'm not sure. The original model
> > matrices
> are available as the X and Zt (transpose of Z) slots. The
> >
> (transpose of the) derived model matrix for the orthogonal random
> > effects is available as A. The terms attribute of the model matrix
> X
> > and the assign attribute of the model frame (in the slot
> named
> > "frame") should be used to associate terms with
> columns of the model
> > matrix.
> >
> > It's
> possible that the calculation would be straightforward. As i
> >
> said, I don't know. My gut feeling is that it is not, which is why I
> > haven't embarked on it.
> >
> >
> _______________________________________________
> >
> R-sig-mixed-models at r-project.org mailing list
> >
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >
>
>
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--
Andrew Robinson
Department of Mathematics and Statistics Tel: +61-3-8344-6410
University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599
http://www.ms.unimelb.edu.au/~andrewpr
http://blogs.mbs.edu/fishing-in-the-bay/
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