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

[Peter Dalgaard]

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"))
> # 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? 
>   

The issue is that you are using marginal tests which will do strange
things when contrasts are not coded "right", and in particular treatment
contrasts are not. Switch to e.g. contr.helmert and the results become
similar. Marginal tests of main effects in the presence of interaction
is not necessarily a good idea and they have been debated here and
elsewhere a number of times before. People don't agree entirely, but the
dividing line is essentially whether it is uniformly or just mostly a
bad idea. It is essentially the discussion of type III SS.

> fortune("type III")

Some of us feel that type III sum of squares and so-called ls-means are
statistical nonsense which should have been left in SAS.
   -- Brian D. Ripley
      s-news (May 1999)


> Thanks a lot!
> Karl
>
>
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>
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>   


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   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
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