hayesall / nuMoM2b_preprocessing

φ Preprocessing scripts to create reproducible partitions of the nuMoM2b data set. Part of the Indiana University Precision Health Initiative.

nuMoM2b Preprocessing — Precision Health Initiative (φ)

A module for creating reproducible partitions of the nuMoM2b data set based on configuration files.

• Maintained by Alexander L. Hayes
• Documentation on https://doc.numom2b.org/en/latest/

Getting Started

Data should not be stored here.

Familiarity with Python, UNIX systems, and Git would be helpful.

Getting Organized

The running assumption is that Data/ contains the .csv files representing the data set, and this nuMoM2b_preprocessing/ repository contains the code and documentation.

Each might be stored as follows (though this may be tweaked through config files):

Precision-Health-Initiative/
├── Data/
│   ├── pregnancy_outcomes.csv
│   ├── Screening.csv
│   └── Visit1.csv
└── nuMoM2b_preprocessing/
    └── README.md

Getting Running

Clone the repository from GitHub:

git clone [e-mail]:hayesall/nuMoM2b_preprocessing.git

If you're using Anaconda, this would be a good time to create an environment:

conda create -n PHI python=3.7

... and install dependencies.

pip install -r phi/requirements.txt

Using nuMoM2b_preprocessing

• As a Package

  Installing using the setup script adds a numom2b_preprocessing package.

  python setup.py install

  ... which can then be imported

  import numom2b_preprocessing
  
  _params = numom2b_preprocessing.parameters(config="phi_config.json")
  numom2b_preprocessing.run(_params)

• As a Commandline (CLI) Tool

  Installing using setup.py adds an entry point to your default bin/ directory.

  python setup.py install

  This adds a numom2b_preprocessing tool which can be invoked as follows:

  numom2b_preprocessing --help

• As a Submodule

  nuMoM2b_preprocessing acts as the first step in building classification pipelines. To incorporate it in later learning steps, it may be useful to have access to the methods as a submodule. For general documentation on using submodules, refer to the Git Manual.

  git submodule add [e-mail]:hayesall/nuMoM2b_preprocessing.git

  The modules in the package can then be accessed as normal.

  import nuMoM2b_preprocessing.numom2b_preprocessing
  
  _params = numom2b_preprocessing.parameters(config="phi_config.json")
  numom2b_preprocessing.run(_params)

nuMoM2b_preprocessing Documentation

Documentation is not currently hosted at https://doc.numom2b.org/en/latest/, but local copies may be built using Sphinx.

A separate requirements file is in the documentation/ directory.

pip install -r documentation/requirements.txt

A make.bat and Makefile are included:

cd documentation
make html

If the build is successful, a copy will reside in a new build/html/ directory.

open build/html/index.html          # (macOS)
xdg-open build/html/index.html      # (Linux — "should" open with default browser)