[Biopython-dev] Statistics code

[Peter Cock]

On Thu, Apr 3, 2008 at 10:49 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> >  But I think that I will need to use more stats stuff as I implement functionality.
>
>  One solution is just to copy and paste whatever statistics code you need from S
>  SciPy.

That does seem to be an option based on their licence and Biopython's.

>  > I think that NumPy has only basic stuff (standard deviation, mean). I
>  > might be wrong, but my research points to that.

According to http://www.scipy.org/Numpy_Functions_by_Category they
have array statistics: average(), mean(), bincount(), histogram(),
corrcoef(), cov(), max(), min(), ptp(), median(), std(), var() plus a
selection of random number and distribution functions.

>  The ideal solution would be to move the statistics stuff from SciPy to NumPy,
>  or to expand the statistics stuff currently in NumPy. Since SciPy and NumPy
>  come from the same group of developers, they may not mind too much.

Is that something you want to raise with them, Michiel?

>  Having a statistics library in NumPy would be a big encouragement to move from
>  Numeric to NumPy.

Speaking of which, is that still stuck on the 64bit issue?
Bug 2251 - NumPy support for BioPython
http://bugzilla.open-bio.org/show_bug.cgi?id=2251

Peter