R help - Feb 2014 - What is the effect of how.many in the "contrast" function

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
help.



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There is no contrast() function in R itself, but this seems to be about 
contrasts().

On 14/02/2014 04:35, jimj wrote:
> 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
> help.
You should always read the help page, which does explain this.  Maybe 
you need the background of Chapter 6 of MASS (the book)?
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
Please do.  Had you shown an example we could probably have explained 
this to you.


-- 
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)
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