mynhanes 0.2.2

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User Guide: MyNHANES

Introduction

Welcome to MyNHANES, a powerful tool designed to facilitate the management and analysis of NHANES data. MyNHANES provides an integrated environment to manage master data, work processes, and apply transformations on NHANES datasets. This guide will help you get started with installing MyNHANES, setting up your environment, and using its key features.

Installation

To install MyNHANES, we recommend using Python 3.12 or above. Follow these steps:

1. Create a virtual environment (optional but recommended):

   python -m venv mynhanes_env
   source mynhanes_env/bin/activate  # On Windows use `mynhanes_env\Scripts\activate`
   

2. Install MyNHANES via pip:

   pip install mynhanes
   

Initial Setup

After installation, navigate to the package directory and run the following command to set up the database, create a user, and load the master data and global transformation rules:

cd path_to_mynhanes_package  # Replace with the actual path
python manage.py deploy --type local

This command will initialize the SQLite database and populate it with the necessary data.

Running the Web Server

Once the setup is complete, you can start the web server to access the MyNHANES system via a web browser:

python manage.py runserver

Visit http://127.0.0.1:8000/admin in your web browser to log in and begin using MyNHANES.

Core Modules

Master Data Management

MyNHANES uses master data such as cycles, datasets, variables, and tags to organize NHANES data. These elements are crucial for managing and navigating the data efficiently.

• Cycles: Represent different NHANES survey periods.
• Datasets: Collections of data for each cycle.
• Variables: Individual variables within the datasets.
• Tags: Used to categorize and filter datasets and variables.

WorkProcess

The WorkProcess module manages the lifecycle of datasets, from downloading to processing.

• Activating a Dataset: In the admin interface, you can activate datasets for download by setting their status and managing their lifecycle.
• Ingestion: Once a dataset is activated, you can ingest the data into the system for further analysis.

Transformations

Transformations allow you to apply predefined rules to the NHANES data, modifying or normalizing it for analysis.

• Running Transformations: Transformations can be triggered through the admin interface, where you select the relevant rules to apply to the data.
• Custom Rules: You can create and manage custom transformation rules based on your analytical needs.

Queries and Data Export

MyNHANES provides tools for creating dynamic queries and exporting the results.

• Query Builder: Use the query builder to define custom queries across cycles, datasets, and variables.
• Data Export: Export query results to CSV or other formats directly from the admin interface.

Storage

MyNHANES uses SQLite as the default database for storing all data, which makes it easy to manage and share data files.