Preprocessing

The preprocessing notebook for the American Gut data. A version of the notebook text can be found on [google docs](https://docs.google.com/document/d/1AR2GrHsVT8LjVTiRHPnn43GF_Eoz8wT5ZH3Q-Of9-BI/edit?usp=sharing). 
"To change where data is saved, the <code>base_dir</code> should be set." -> "To change where data is saved, modify the value of <code>base_dir</code>."

You are already setting it...