search

biocore / mds-approximations

Multidimensional scaling algorithms for microbiology-ecology datasets.
6 stars 7 forks source link

WIP: Cogent porrt #10

Closed mortonjt closed 9 years ago

mortonjt commented 9 years ago

Here's a complete port over of both scmds and nystrom from pycogent.

I haven't included numpy docs for approximate_mds.py or goodness_of_fit.py. Do we really care?

Here, I created a really barebone wrapper function for scmds and nystrom, to make standardizing these function calls more straightforward.

mortonjt commented 9 years ago

Also, would anyone opposed to making skbio a dependency? I personally like some of the testing utils.

antgonza commented 9 years ago

fine with me.

ElDeveloper commented 9 years ago

Fine with me as well.

mortonjt commented 9 years ago

:boom: Tests passing

antgonza commented 9 years ago

I think the code looks fine, note that this has been reviewed a few times before. However, it's not skbio ready but I think we shouldn't spend time on this and simply benchmark, then clean the code that is actually gonna be moved to skbio. Thus, merging.