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nuMoM2b_preprocessing

A Python package for pre-processing nuMoM2b data with configuration files.

Documentation Status Build Status Code Coverage Config file image.

This is one component within a wider research project for predicting adverse events over the course of a woman's pregnancy. This package serves the dual role of assisting with pre-processing tasks and for producing reproducible partitions of the data based on configuration files.

.. toctree::
   :maxdepth: 1
   :hidden:
   :caption: Getting Started:

   getting_started
   architecture
   first_config

.. toctree::
   :maxdepth: 1
   :hidden:
   :caption: API:

   api/numom2b_preprocessing
   api/numom2b_preprocessing.get_config
   api/numom2b_preprocessing.preprocess

.. toctree::
   :glob:
   :maxdepth: 1
   :hidden:
   :caption: Sample Config Files:

   config_files/*

.. toctree::
  :hidden:
  :caption: External Links

  GitHub Repository <https://github.com/hayesall/nuMoM2b_preprocessing>
  Bug Tracker <https://github.com/hayesall/nuMoM2b_preprocessing/issues>

Maintained by Alexander L. Hayes, a Ph.D. student with the Indiana University ProHealth Group working on the Precision Health Initiative (φ). Alexander can be reached at hayesall@iu.edu.

Getting Started

Pointers for getting nuMoM2b_preprocessing working on your local machine.

Architecture

High-level overview of how this project is organized.

nuMoM2b_preprocessing architecture.

Writing Configuration Files

Configuration files define which variables should be used and how they should be aggregated. This is a worked example for writing a configuration file.

{
  "csv_path": "../FullData/numom_data/",
  "target": {
      "name": "Ancillary/Pregnancy_outcomes.csv",
      "variables": ["PublicID", "oDM"]
  },
  "files": [
    {
      "name": "Screening_Admin_Visits/Visit1.csv",
      "variables": ["PublicID", "V1BA01_KG", "V1BA01_LB"]
    }
  ]
}

Indices and tables

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