[R] Contrast specified with C() - R vs S-Plus problem

[Prof Brian Ripley]

On Wed, 8 Oct 2003, Pascal A. Niklaus wrote:

> Thanks for the reply. Below is the solution and the S-Plus and R code
> that does the same (for documentation).
> 
> >I can't reproduce that in S-PLUS 6.1, and it is not as documented:
> >  
> >
> In S-Plus 2000, C() complements the contrast matrix with orthogonal 
> contrasts if only the first is given.

And so does R.  You just did not specify it correctly in R.  The code you 
quote works in R as well, but your original example had four levels, not 
three.

>  CO2 <- factor(rep(c("A","C","E"),each=8))
> m <- rep(seq(0,3,length=8),3) + rep(c(0,1,2),each=8)
> summary.aov(aov(m ~ C(CO2,c(1,0,-1))))
                    Df Sum Sq Mean Sq F value   Pr(>F)
C(CO2, c(1, 0, -1))  2 16.000   8.000  7.2593 0.004014
Residuals           21 23.143   1.102

Please do not make out your user errors to be S-R differences.
Did you actually try your example in R?

> > CO2 <- factor(rep(c("A","C","E"),each=8))
> 
> > m <- rep(seq(0,3,length=8),3) + rep(c(0,1,2),each=8)
> 
> > summary.aov(aov(m ~ C(CO2,c(1,0,-1))))
> 
>                     Df Sum of Sq  Mean Sq  F Value       Pr(F)
> 
> C(CO2, c(1, 0, -1))  2  16.00000 8.000000 7.259259 0.004013532
> 
>           Residuals 21  23.14286 1.102041
> 
> > summary.lm(aov(m ~ C(CO2,c(1,0,-1))))
> 
> Coefficients:
> 
>                         Value Std. Error  t value Pr(>|t|)
> 
>          (Intercept)   2.5000   0.2143    11.6667   0.0000
> 
> C(CO2, c(1, 0, -1))1  -1.0000   0.2624    -3.8103   0.0010
> 
> C(CO2, c(1, 0, -1))2   0.0000   0.3712     0.0000   1.0000
> 
> Residual standard error: 1.05 on 21 degrees of freedom
> 
> Multiple R-Squared: 0.4088
> 
> F-statistic: 7.259 on 2 and 21 degrees of freedom, the p-value is 0.004014
> 
> Correlation of Coefficients:
> 
>                      (Intercept) C(CO2, c(1, 0, -1))1
> 
> C(CO2, c(1, 0, -1))1 0
> 
> C(CO2, c(1, 0, -1))2 0           0
> 
>
-- 
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