[R-lang] contrast coding

[Bob Slevc]

Hi there R-language-gurus,

I have what I think is a simple question – maybe even a stupid  
question (and there are too stupid questions) – that's related to  
recent discussions on this list.  Imagine, if you will, that I have a  
full-factorial design, and want to set up a set of orthogonal  
contrasts rather than using R's default dummy coding.  For a simple  
2x2 design, I want something like this, where contrasts 1 and 2 are  
the main effects for A and B, and contrast 3 is the interaction:

			a1	a1	a2	a2
			b1	b2	b1	b2
contrast1	1	1	-1	-1
contrast2	1	-1	1	-1
contrast3	1	-1	-1	1

I haven't found any contrast function (e.g., contr.poly / contr.sum /  
etc.) that'll automatically create a matrix for this kind of  
contrast, but can I just specify the individual factor contrasts and  
assume that R will just multiply them to give nice orthogonal  
interaction contrasts?  For example, if my factors are called A and  
B, and I say:

contrasts(datafile$A) <- c(1,-1)
contrasts(datafile$B) <- c(1,-1)

and then run a model (on log(RTs) apparently):

model <- lmer(log(RT) ~ A*B + (1|subj) + (1|item), data=datafile)

Then am I set?  I'm a little unsure, partially because it gives me  
slightly different results than the default dummy coding does (though  
it does seem to be orthogonal as the correlations between fixed  
effects are all zero...)

Thanks much,
Bob

---
L. Robert (Bob) Slevc, Ph.D.
Rice University, Dept. of Psychology • 6100 Main Street • Houston, TX  
77005
http://www.ruf.rice.edu/~slevc/

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