This section describes how to get organized and get the code running. This will try to keep concepts as accessible as possible, but some familiarity with Python projects, UNIX systems, and Git would certainly be helpful.
The running assumption will be that the nuMoM2b data is contained in a directory (likely unzipped from a
numom2b.zip), and this
nuMoM2b_preprocessing/ repository is available on your local machine.
For example, we find it helpful to organize work as follows (though these may be tweaked with config files):
Precision-Health-Initiative/ ├── Data/ │ ├── pregnancy_outcomes.csv │ ├── Screening.csv │ └── Visit1.csv └── nuMoM2b_preprocessing/ ├── README.md └── numom2b_preprocessing/
nuMoM2b_preprocessing may be cloned from GitHub:
git clone https://github.com/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 conda activate PHI
… and install dependencies.
pip install -r numom2b_preprocessing/requirements.txt
A separate requirements file is in the
pip install -r documentation/requirements.txt
Makefile are included:
cd documentation make html
If the build is successful, a copy will reside in a new
open build/html/index.html # (macOS) xdg-open build/html/index.html # (Linux)