I have been trying for hours now to perform an orthogonal contrast through an
ANOVA in R.
I have done a two-factor factorial experiment, each factor having three
levels. I converted this dataset to a dataframe with one factor with nine
treatments, as I couldn't work out what else to do.
I have set up a matrix with the eight orthogonal contrasts that I wish to
perform, but despite having searched this mailing list's archives
thoroughly, I cannot get it to work.
I am looking to get output along the lines of
Df Sum Sq Mean Sq F value Pr(>F)
trt1 1 X X X X
trt2 1 X X X X
...............
trt9 1 X X X X
Residuals 27 495.1 18.3
However, for everything I've tried, I've simply gotten
Df Sum Sq Mean Sq F value Pr(>F)
trt 8 17919.7 2240.0 122.16 < 2.2e-16 ***
Residuals 27 495.1 18.3
I have done
trt <- as.factor(trt)
contrasts(trt) <- cntrs
when I then type contrasts(trt), it returns what I expect.
However, whether I try
test <- aov(time2 ~ trt)
test <- aov(time2 ~ trt, contrasts=contrasts(trt))
test <- aov(time2 ~ C(trt, cntrs, how.many=8))
or anything else I can think of, I only get what I posted above. I'm
assuming I'm doing something fundamentally wrong, but for the life of me I
can't work out what, and it's killing me at present.
Any responses would be greatly appreciated
Marc Burgess
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