Initial commit
Initial commit of messy code, specific to microbiomic data.
Update README.md
Merge pull request #1 from jrrideout/test-branch

Update README.md
Merge pull request #2 from rybern/master

Initial commit of messy code, specific to microbiomic data.
Added a script command line and settings file interface, starting to refactor code
Added flexiblity (nothing is now specific to microbiomic data)
Added functionality (feature vector reporting)
Refactored some of the more complex parts
Removed outdated sections

Not yet ready for use. Still need to finish documentation and refactoring sections.
removed old file
Added documentation
Added plot.py, added file support, added testing (without test partition), added minerva results, added minerva scripts (previous run)
Merge pull request #3 from rybern/code-cleanup

Code cleanup
Remove extraneous files
Delete blank config file

Not necessary as this can be generated from script.py
Update README.md with dep info
Improve script.py documentation a bit

Mainly to help myself keep everything straight in my head
Update code to work with sklearn 0.14.1

Fixes an error when running random forest and also a DeprecationWarning.
Output files are now correctly closed.
Add test data and update README with instructions
Merge pull request #4 from jrrideout/cleanup

Some initial cleanup and test data
Did significant refactoring on most sections. Also sped up analysis by roughly 3-fold.