R help - Jun 2007 - aov and lme differ with interaction in oats example of MASS?

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? 

Thanks a lot!
Karl


      __________________________________  Alles was der Gesundheit und
Entspannung dient. BE A BETTER MEDIZINMANN! www.yahoo.de/clever

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
>
>
>       __________________________________  Alles was der Gesundheit und
Entspannung dient. BE A BETTER MEDIZINMANN! www.yahoo.de/clever
>
> ______________________________________________
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> and provide commented, minimal, self-contained, reproducible code.
>   

-- 
   O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907

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)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595