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From Bob MacCallum <r.maccal...@imperial.ac.uk>
Subject Re: [math] ANOVA proposal
Date Wed, 14 Nov 2007 14:31:01 GMT

Ok, thanks for the advice, Niall.

Please see https://issues.apache.org/jira/browse/MATH-173

Shame I already signed up to bugzilla...


Niall Pemberton writes:
 > On Nov 14, 2007 1:41 PM, Bob MacCallum <r.maccallum@imperial.ac.uk> wrote:
 > >
 > > Hello,
 > >
 > > The org.apache.commons.math.stat.* packages are exactly what we need for our
 > > microarray analysis web application except for the lack of an ANOVA class (the
 > > FDistribution is already there however).  I have coded this up and it seems to
 > > produce the same output as R's anova(lm(data)) - as described in more detail
 > > in the test suite.
 > >
 > > I have added the following to my anonymous SVN checkout:
 > >
 > > src/test/org/apache/commons/math/stat/inference/AnovaTest.java
 > > src/java/org/apache/commons/math/stat/inference/Anova.java
 > > src/java/org/apache/commons/math/stat/inference/AnovaImpl.java
 > >
 > > Should I add this to a bugzilla ticket for you guys to look at?
 > 
 > Thats the best way - although we use Jira rather than bugzilla:
 > 
 > http://commons.apache.org/math/issue-tracking.html
 > 
 > > How do I get
 > > a suitable patch file?  If I do svn diff, these new files are not in
 > > subversion...  Or should I just tar up these files?
 > 
 > You could do an svn add to your local copy and then create a patch
 > file but IMO for new files best to just attach them directly to the
 > Jira ticket (theres a "multiple files" option that allows you to do
 > three at a time).
 > 
 > Niall
 > 
 > > I guess one issue is naming... Should it be called UnivariateAnova, for
 > > example?
 > >
 > > Here are the methods from interface definition as a taster.
 > > As you can see, I need to flesh out the documentation some more.
 > >
 > >     /**
 > >      * Computes the ANOVA F-value for a set of data in two or more classes.
 > >      *
 > >      * @param classdata  Hashtable - key = classname, values = double[]
 > >      * @return Fvalue
 > >      * @throws IllegalArgumentException if the precondition is not met
 > >      * @throws MathException if the statistic can not be computed do to a
 > >      *         convergence or other numerical error.
 > >      */
 > >     public abstract double anovaFValue(Hashtable classdata)
 > >         throws IllegalArgumentException, MathException;
 > >
 > >     /**
 > >      * Computes the ANOVA P-value for a set of data in two or more classes.
 > >      *
 > >      * @param classdata  Hashtable - key = classname, values = double[]
 > >      * @return Pvalue
 > >      * @throws IllegalArgumentException if the precondition is not met
 > >      * @throws MathException if the statistic can not be computed do to a
 > >      *         convergence or other numerical error.
 > >      */
 > >     public abstract double anovaPValue(Hashtable classdata)
 > >         throws IllegalArgumentException, MathException;
 > >
 > >
 > > I have followed TTest as a style guide.
 > >
 > > cheers,
 > > Bob.
 > >
 > >
 > > --
 > > Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
 > > Division of Cell and Molecular Biology | Imperial College London |
 > > Phone +442075941945 | Email r.maccallum@imperial.ac.uk
 > >
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 > >
 > >
 > 
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 > 

-- 
Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups |
Division of Cell and Molecular Biology | Imperial College London |
Phone +442075941945 | Email r.maccallum@imperial.ac.uk

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