README.md

Welcome to pytexmex, a Python 3 implementation of R package texmexseq

Treatment Effect eXplorer for Microbial Ecology eXperiments (texmex) is designed to normalize OTU count data and correct for community composition changes that are common to a control and experimental unit.

• author: Scott Olesen (swo at mit dot edu)
• project page: https://almlab.mit.edu/texmex.html
• python github: https://github.com/swo/texmexseq
• R github: https://github.com/swo/texmexseq,
• R CRAN page: http://cran.r-project.org/web/packages/texmexseq/index.html

Getting started

Read the documentation.

Check out the demo script under demo/, which uses the demo data in data/.

Installation

I'm not sure the package is fully functional. You can set it up in "development" mode with:

python3 setup.py develop

After that, you should be able to import pytexmex and get everything. If you want to "unlink" this development version, you can

python3 setup.py develop --uninstall

todo

• Check the values I compute against Bulmer's values (i.e., the ones in macroecotools)
• Clean up documentation (and this and this)
• Write some nicer documentation intro
• Make the package structure correct
• Make sure the __init__.py files are correct
• The pp_plot_data is slow because it computes so many pmf's. There's probably a good way to start approximating the values for high n.
• Package the poilog functions into a scipy-style distribution