[R] What is the effect of how.many in the "contrast" function

jimj jimj at sfu.ca
Fri Feb 14 05:35:39 CET 2014

I have been asked to see if there is a linear trend in 3 groups of data (5
points each) by using ANOVA and linear contrasts. The 3 groups represent
data collected in 2010,2011 and 2012. I want to use R for this procedure and
I have tried both of the following:  

    contrasts(data$groups, how.many=1) <- contr.poly(3)
contrasts(data$groups)  <- contr.poly(3)

Both ways seem to work fine but give slightly different answers in terms of
their p-values. I have no idea which is correct and it is really tricky to
find help for this on the web. I would like help figuring out what is the
reasoning behind the different answers. I'm not sure if it has something to
do with partitioning sums of squares or whatnot. Thanks so much for your

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