[SciPy-Dev] Van der Waerden test in Scipy?

[Annalisa Minelli]

Hi Josef, hi all,
thanks for answering and thanks for the questions/hints..

2011/6/1 <josef.pktd at gmail.com>

> On Wed, Jun 1, 2011 at 3:56 AM, Annalisa Minelli <annalisa.py at gmail.com>
> wrote:
> > Dear Scipy developers,
> > I'm Annalisa Minelli, a PhD student from Perugia (Italy), and I'm using
> > Scipy library because I'm writing some code for my PhD thesis.
> > Since I needed van der waerden chisquare pvalue[0], which is implemented
> in
> > R but not in Scipy (if I'm not wrong)[1], I implemented the test in
> python
> > language [3] to break any R dependency for my module.
> >
> > So if you think it can be useful, maybe it could be integrated into the
> > Scipy library?
> > Could you give me any advice on how to proceed?
>
> Thanks Annalisa,
>
> I think it would be useful to have this test (and similar tests based
> on transformation to the normal distribution).
>
> I downloaded your vdw.py. I haven't looked at the details yet, but
> here are 3 main issues:
>
> your vdw is GPL which is incompatible with scipy's BSD license, for
> inclusion in scipy it would need to be a contribution licensed as BSD
>

ok, I suppose I can change the license. I initially made this choice because
I need this function into a GRASS GIS module - r.broscoe [0] and the Project
uses GPL, but for sure I'd like to include the function in the Scipy library
(which is used by GRASS).


> your function is not using numpy, and it seems to me that many of the
> list operations can be vectorized with numpy
>

ok, I'll try this way if you think it's better; I initially thought that the
less dependencies was the best, but if you think I can considerably hack the
code in this way, I will do it.

>
> no tests: since you have the equivalent function in R, it would be
> good to add some tests that have results from R to check that the
> function produces the same results. ( for explanation and examples:
> https://github.com/numpy/numpy/blob/master/doc/TESTS.rst.txt or look
> in scipy.stats.tests )
>

thanks for the hint; the pics I reported in my blog are from a run that
takes in input the example data.frame of R for the equivalent waerden.test
function (the data.frame is "sweetpotato") - with the only difference that
my function uses numbers for groups instead of strings (maybe I can fix
this..) but I'll do more tests, following numpy tests "standards" - thank
you

>
> additional: docstring should follow the numpy standard, see examples
> in current functions and
>
> https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt#docstring-standard
>

ok, I'll fix these issues and come back in list ;-)

Cheers,
Annalisa


[0]: https://svn.osgeo.org/grass/grass-addons/vector/v.strahler/



>
> How to proceed if these issues are addressed:
> Since it is a new function, it would be easy to integrate it into
> scipy from the python files, but if you are familiar with git and
> github, the integration will eventually be easier if you fork scipy
> and add the function to scipy.stats and make a pull request.
> A trac ticket would also be useful to keep track of the contribution
> (I don't know if github will substitute for this).
> At the beginning, it might be easiest to discuss this on the mailing list.
>
> Cheers, and thanks for any contributions,
>
> Josef
>
> >
> > Best Regards,
> > Annalisa Minelli
> >
> >
> > [0]: http://en.wikipedia.org/wiki/Van_der_Waerden_test
> > [1]:
> http://rss.acs.unt.edu/Rdoc/library/agricolae/html/VanderWarden.html
> > [2]:
> http://amirror4thesun.blogspot.com/2011/05/van-der-waerden-test.html
> >
> > _______________________________________________
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> > SciPy-Dev at scipy.org
> > http://mail.scipy.org/mailman/listinfo/scipy-dev
> >
> >
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