redcap-eda 0.2.0

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, visualization, and report generation.

🚀 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, word clouds)
• 📂 Comprehensive PDF Report Generation with UnifiedReport
• 🔄 Multiprocessing for Faster Execution
• 🔍 Progress Bars with tqdm
• 📂 Exports Reports (JSON, PDF, and saved visualizations)
• 📝 Interactive Schema Creation for custom datasets

📦 Installation

pip install redcap-eda

🛠️ Usage

🔹 Example Using the Sample Dataset and Interactive Schema Creation

redcap-eda analyze --sample

🔹 Example Using the Sample Dataset with a Predefined Schema

redcap-eda analyze --sample --sample-schema

🔹 Running EDA on a Custom Dataset with Interactive Schema Creation

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

🔹 Running EDA on a Custom Dataset with a Predefined Schema

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

🔹 Running in Debug Mode

redcap-eda --debug analyze --sample

🔹 Listing Available Test Cases

redcap-eda list-cases

📂 Project Structure

.
├── Makefile                # Helper commands
├── README.md               # Project documentation
├── dist                    # Distribution files for PyPI
├── 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
│       ├── analysis        # EDA analysis modules
│       │   ├── categorical
│       │   │   └── mixins.py # Categorical data analysis
│       │   ├── datetime
│       │   │   └── mixins.py # Datetime data analysis
│       │   ├── eda.py      # Main EDA module
│       │   ├── json_report_handler.py # JSON export utility
│       │   ├── lib.py       # Shared data structures (e.g., AnalysisResult)
│       │   ├── missing
│       │   │   └── mixins.py # Missing data analysis
│       │   ├── numerical
│       │   │   └── mixins.py # Numerical data analysis
│       │   └── text
│       │       └── mixins.py # Text data analysis
│       ├── cast_schema.py  # Schema enforcement
│       ├── cli.py          # Command-line interface
│       ├── load_case_data.py # Dataset loader
│       ├── logger.py       # Logging utilities
│       └── unified_report.py # PDF report generation
└── 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!