search

qiime2 / q2-diversity

BSD 3-Clause "New" or "Revised" License
4 stars 45 forks source link

Added jensenshannon metric #271

Closed patrickimran closed 4 years ago

patrickimran commented 4 years ago

This PR just adds another non-phylogenetic metric, Jensen Shannon distance, to the set of non_phylogenetic_metrics. It is one of those additional metrics implemented in scipy.spatial.distance.pdist which can be passed to skbio.diversity.

thermokarst commented 4 years ago

Thanks @patrickimran! @ChrisKeefe is currently working on moving most (all?) of these metrics out into a new standalone plugin (https://github.com/qiime2/q2-diversity-lib). @ChrisKeefe - how do you want to address integrating the changes proposed in this PR?

ChrisKeefe commented 4 years ago

Thanks for the contribution, @patrickimran ! I don't think q2-diversity-lib is quite ready for outside contributions yet, but :crossed_fingers: that should change in the next month or two. I think it's best to bring this into q2-diversity for now, and I can port it over to diversity-lib later. Or you can, if that would bring you joy :wink:

If you're interested in contributing diversity measures to q2-diversity-lib in the future, we would love the support. div-lib allows us to provide measures as individual Actions, with more robust testing, more flexible semantic typing, individualized citations and documentation, and other niceties. Let me know. :frog: