Warren suggested three ways to tackle this problem:Dear all,As suggested in this github issue (https://github.com/scipy/scipy/issues/3870), I would like to discuss the merit of introducing a new function nanpdist into scipy.spatial. I have also brought up the problem in the following previous e-mail (http://comments.gmane.org/gmane.comp.python.scientific.devel/18956) and on SO (http://stackoverflow.com/questions/24781461/compute-the-pairwise-distance-in-scipy-with-missing-values).
- Don't change anything--the users should clean up their data!
nanpdist
- Add a keyword argument to
pdist
that determines hownan
should be treated.Clearly, I don't favor the first option since I believe missing values can be important pieces of information, too. I slightly tend towards option two because adding a keyword will further complicate an already very long pdist function.
I'm happy to submit a pull request if there is a consensus that something should be done.
Best,
Moritz
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