[R] aov function syntax

[Prof Brian Ripley]

What are you trying to do?  Your example is not what is commonly 
called ANOVA (some call it ANCOVA) and more often lm() is used.

I suspect that you intended 'population' to be a factor, and it is 
not.  So population:condition is not an interaction but different 
slopes for population by levels of condition.

population*condition expands to

population + condition + population:condition

and this is a larger model with different intercepts by levels of 
condition.

I suggest you need study the primary reference (Chambers & Hastie 
1992) or at least Bill Venables' exposition in MASS (the book, any 
edition).  And note that you cannot test interactions in a two-way 
layout without replication, so perhaps you also need to talk to a 
statistician about ANOVA.

BTW: I think you have messed up your first example: perhaps you meant

studentDataSource="http://files.davidderiso.com/r/studentData.data"

There are no P values in that example because there is no residual 
variation: the model fits exactly.

On Sat, 9 Jan 2010, Dave Deriso wrote:

> Hello,
>
> I have a simple question about using the aov function syntax (ie. * + or :)
> for the interaction of 2 factors. I have read the help files, and researched
> other sites, and have included my source files. My goal is to measure the
> signifigance of the interaction between population and condition (aka.
> population:condition). I can't seem to figure it out.
>
> 1. In the first example the significance of population:condition works with
> the "allData" but not with the "studentData." Can you please explain why it
> fails and how I can fix it?
>
> 2. In the second example I can get the measure the significance of
> population:condition with 2 different methods, but I get 2 different results
> (using the "allData" source). Can you please explain why these Pr(>F) values
> are different?
>
> Thank you so much for your help!!
>
> Sincerely,
>
> Dave Deriso
> UCSD Psychiatry
>
>
> #Example 1 ---------------------------COPY & PASTE THE FOLLOWING
>
> #import the data
> allDataSource="http://files.davidderiso.com/r/allData.data"
> allData.import=read.table(allDataSource,header=T)
> studentDataSource="http://files.davidderiso.com/r/allData.data"
> studentData.import=read.table(studentDataSource,header=T)
>
>
> #aov for allData WORKS
> allData.integral.aov = aov(integral~population*condition,
> data=allData.import)
> summary(allData.integral.aov)
>
> #aov for studentData DOES NOT GIVE Pr(>F) of population:condition
> studentData.integral.aov = aov(integral~population*condition,
> data=studentData.import)
> summary(studentData.integral.aov)
>
>
>
> #Example 2 ---------------------------COPY & PASTE THE FOLLOWING
>
> #population:condition has a Pr(>F) of 0.96372
> allData.integral.aov = aov(integral~population*condition,
> data=allData.import)
> summary(allData.integral.aov)
>
> #population:condition has a Pr(>F) of 1.070e-06 ***
> allData.integral.aov = aov(integral~population:condition,
> data=allData.import)
> summary(allData.integral.aov)
>
> 	[[alternative HTML version deleted]]
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
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