BioStatica

BioStatica - Quarto Book Edition

A comprehensive, beginner-friendly biostatistics textbook built with Quarto, offering structured learning from foundational principles to modern methodologies used in cutting-edge research.

🚀 Quick Start

View the Book Online

Visit: https://pawanramamali.github.io/BioStatica/

Build Locally

Prerequisites

• Quarto (latest version)
• R (optional, for R code examples)
• Python (optional, for Python code examples)

Quick Build

# Clone the repository
git clone https://github.com/PawanRamaMali/BioStatica.git
cd BioStatica

# Build the book
quarto render

# View locally
# Open _site/index.html in your browser

Platform-Specific Build Scripts

• Linux/macOS: ./build.sh
• Windows: build.bat

📚 Book Structure

The book is organized into separate Quarto markdown files for optimal maintainability:

BioStatica/
├── _quarto.yml              # Main configuration
├── index.qmd                # Preface and introduction
├── introduction.qmd         # Welcome to Biostatistics
├── ch01-foundational-concepts.qmd
├── ch02-comparative-inference.qmd
├── ch03-multi-group-analysis.qmd
├── ch04-interrelationships-modeling.qmd
├── ch05-design-power-considerations.qmd
├── ch06-specialized-modern-methods.qmd
├── references.qmd           # Bibliography and resources
├── references.bib           # BibTeX references
├── styles.css              # Custom styling
├── custom.scss             # SCSS theme customization
└── _site/                  # Generated website (after build)

📖 Table of Contents

Introduction: Welcome to Biostatistics

Understanding the role of biostatistics in medical research

Chapter 1: Foundational Concepts

• Descriptive Statistics & Visualization
• Probability & Distributions
• Sampling & Sampling Distributions
• Point & Interval Estimation
• Hypothesis Testing Framework
• One-Sample & Two-Sample t-Tests

Chapter 2: Comparative Inference

• Welch’s t-Test & Paired t-Test
• Non-Parametric Alternatives

Chapter 3: Multi-Group Analysis

• One-Way ANOVA
• Post-hoc Comparisons
• Two-Way ANOVA
• Multiple Comparisons

Chapter 4: Interrelationships & Modeling

• Correlation Analysis
• Simple Linear Regression
• Multiple Regression
• Logistic Regression

Chapter 5: Design & Power Considerations

• Sample Size Calculation
• Statistical Power
• Multiple Testing Corrections

Chapter 6: Specialized & Modern Methods

• Survival Analysis
• Causal Inference
• Missing Data & Imputation
• Meta-Analysis
• Bayesian Methods
• Machine Learning & High-Throughput Data

🔧 Development

File Organization

• Content: Each chapter is a separate .qmd file for easy editing and collaboration
• Configuration: _quarto.yml contains all book settings and navigation
• Styling: Custom themes in custom.scss and styles.css
• References: Bibliography managed in references.bib

Adding New Content

1. Edit the relevant .qmd file
2. Add new references to references.bib
3. Update _quarto.yml if adding new chapters
4. Build and test locally: quarto render

Quarto Features Used

• ✅ Cross-references and citations
• ✅ Interactive code blocks
• ✅ Mathematical notation (LaTeX)
• ✅ Callout boxes for important concepts
• ✅ Responsive web design
• ✅ PDF and ePub export capability
• ✅ Search functionality
• ✅ Dark/light theme toggle

🚀 Deployment

Automatic Deployment

• GitHub Actions: Automatically builds and deploys to GitHub Pages on push to main
• GitHub Pages: Live site at https://pawanramamali.github.io/BioStatica/

Manual Deployment

# Build the book
quarto render

# Deploy to GitHub Pages (if configured)
quarto publish gh-pages

🤝 Contributing

We welcome contributions! Here’s how to get started:

1. Fork the repository
2. Clone your fork: git clone https://github.com/yourusername/BioStatica.git
3. Create a new branch: git checkout -b feature/your-feature-name
4. Edit the relevant .qmd files
5. Test your changes: quarto render
6. Commit your changes: git commit -am 'Add some feature'
7. Push to the branch: git push origin feature/your-feature-name
8. Submit a pull request

Contribution Guidelines

• Follow the existing writing style and formatting
• Test builds locally before submitting
• Add references to references.bib for new citations
• Use appropriate Quarto callouts for important information

📄 Export Formats

The book can be exported to multiple formats:

• HTML (default): Interactive web version with search and navigation
• PDF: Print-ready version with proper formatting
• ePub: E-reader compatible format

To generate specific formats:

quarto render --to html
quarto render --to pdf
quarto render --to epub

🔍 Features

• 📱 Responsive Design: Works on desktop, tablet, and mobile
• 🔍 Full-Text Search: Built-in search functionality
• 🎨 Custom Styling: Professional academic appearance
• 📊 Interactive Elements: Code examples and visualizations
• 📚 Cross-References: Linked figures, tables, and equations
• 🌙 Theme Toggle: Dark and light mode support
• 📖 Table of Contents: Collapsible navigation sidebar
• 🔗 Citations: Proper academic referencing

📊 Technical Details

• Built with: Quarto publishing system
• Theme: Custom Bootstrap-based theme with academic styling
• Fonts: Crimson Text (serif), Source Sans Pro (sans-serif), JetBrains Mono (monospace)
• Math: LaTeX support via MathJax
• Code: Syntax highlighting for R, Python, and other languages

📝 License

This project is licensed under the MIT License - see the LICENSE file for details.

👥 Maintainer

Pawan Rama Mali 📧 Email: prm@outlook.in 🐙 GitHub: PawanRamaMali

🙏 Acknowledgments

• The biostatistics and open science communities
• Quarto development team
• Contributors and reviewers

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Ready to dive into biostatistics? Start reading the book online or build it locally!

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