[R] aov and lme differ with interaction in oats example of MASS?

[Prof Brian Ripley]

On Thu, 28 Jun 2007, Karl Knoblick wrote:

> Dear R-Community!
>
> The example "oats" in MASS (2nd edition, 10.3, p.309) is calculated for aov and lme without interaction term and the results are the same.
> But I have problems to reproduce the example aov with interaction in MASS (10.2, p.301) with lme. Here the script:
>
> library(MASS)
> library(nlme)
> options(contrasts = c("contr.treatment", "contr.poly"))

That is the problem.  You need true contrasts, so use contr.helmert.  When 
I did so I got the same results from lme and aov for the anovas.

The question of what a 'marginal' AoV means without orthogonality is moot.
The sequential version is fine here.

> # aov: Y ~ N + V
> oats.aov <- aov(Y ~ N + V + Error(B/V), data = oats, qr = T)
> summary(oats.aov)
> # now lme
> oats.lme<-lme(Y ~ N + V, random = ~1 | B/V, data = oats)
> anova(oats.lme, type="m") # Ok!
> # aov:Y ~ N * V + Error(B/V)
> oats.aov2 <- aov(Y ~ N * V + Error(B/V), data = oats, qr = T)
> summary(oats.aov2)
> # now lme - my trial!
> oats.lme2<-lme(Y ~ N * V, random = ~1 | B/V, data = oats)
> anova(oats.lme2, type="m")
> # differences!!! (except of interaction term)
>
> My questions:
> 1) Is there a possibility to reproduce the result of aov with interaction using lme?
> 2) If not, which result of the above is the correct one for the oats example?
>
> Thanks a lot!
> Karl

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
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