redcap-eda 0.1.0

Perform exploratory data analysis on REDCap data

REDCap-EDA

📌 Overview

REDCap-EDA is a command-line tool for performing Exploratory Data Analysis (EDA) on REDCap datasets. It automates data inspection, schema enforcement, statistical analysis, and visualization.

🚀 Features

• ✅ Automatic Data Type Enforcement (casts columns based on a predefined or user-defined schema)
• 📊 Summary Statistics (mean, median, std dev, outliers, categorical distributions)
• 📉 Visualizations (histograms, box plots, categorical distributions, time trends)
• 🔄 Multiprocessing for Faster Execution
• 🔍 Progress Bars with tqdm
• 📂 Exports Reports (JSON, CSV, and saved visualizations)
• 📝 Interactive Schema Creation for custom datasets

📦 Installation

# Clone the repository
git clone https://github.com/robertp/REDCap-EDA.git
cd REDCap-EDA

# Install dependencies using Poetry
poetry install

🛠️ Usage

🔹 Example Using the Sample Dataset and Interactive Schema Creation

poetry run redcap-eda analyze --sample

🔹 Example Using the Sample Dataset with a Predefined Schema

poetry run redcap-eda analyze --sample --schema schemas/schema_sample_dataset.json

🔹 Running EDA on a Custom Dataset with Interactive Schema Creation

poetry run redcap-eda analyze --csv path/to/your_data.csv

🔹 Running EDA on a Custom Dataset with a Predefined Schema

poetry run redcap-eda analyze --csv path/to/your_data.csv --schema path/to/schema.json

🔹 Running in Debug Mode

poetry run redcap-eda --debug analyze --sample

🔹 Listing Available Test Cases

poetry run redcap-eda list-cases

🔹 Interactive Testing with Makefile

# Explore a text-based column
make test-text

# Analyze numerical data
make test-numeric

# Inspect categorical variables
make test-categorical

# Run full exploratory analysis interactively
make test-eda

📂 Project Structure

.
├── Makefile                # Helper commands
├── README.md               # Project documentation
├── mypy.ini                # Type checking configuration
├── poetry.lock             # Poetry dependency lock file
├── pyproject.toml          # Poetry project configuration
├── schemas                 # Saved schema files
│   └── schema_sample_dataset.json
├── src
│   ├── logs
│   │   └── redcap_eda.log  # Log files
│   └── redcap_eda
│       ├── __init__.py
│       ├── analysis        # EDA analysis modules
│       │   ├── __init__.py
│       │   ├── categorical
│       │   │   ├── __init__.py
│       │   │   └── mixins.py
│       │   ├── datetime
│       │   │   ├── __init__.py
│       │   │   └── mixins.py
│       │   ├── eda.py      # Main EDA module
│       │   ├── numerical
│       │   │   ├── __init__.py
│       │   │   └── mixins.py
│       │   └── text
│       │       ├── __init__.py
│       │       └── mixins.py
│       ├── cast_schema.py  # Schema enforcement
│       ├── cli.py          # Command-line interface
│       ├── load_case_data.py # Dataset loader
│       ├── logger.py       # Logging utilities
└── tests                   # Unit tests
    ├── __init__.py
    └── fixtures
        └── toy_data.csv    # Sample test data

📝 Contributing

1. Fork the repository and create a feature branch.
2. Run tests to ensure code integrity:

   poetry run pytest tests/
   

3. Submit a pull request with a detailed description.

📜 License

This project is licensed under the MIT License.

🤝 Acknowledgments

• REDCap for enabling structured data collection.
• The Open Source Community for inspiration & contributions!