CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Repository Overview

This is a Quarto-based blog focused on data science, pharmacokinetic modeling, and R tutorials, authored by Granville Matheson. It was successfully migrated from Hugo/blogdown to Quarto in 2024 to fix rendering issues and modernize the tech stack.

Development Environment

Quarto: Primary static site generator
R: For executing code in posts and data analysis
GitHub Actions: Automated deployment pipeline

Common Commands

Local Development

# Preview the site locally with live reload
quarto preview

# Render the entire site
quarto render

# Check for issues
quarto check

# Clear cache if having rendering issues
quarto render --cache-refresh

Content Management

# Add new post (create in appropriate year directory)
mkdir -p posts/2024
touch posts/2024/new-post.qmd

# Add new section
mkdir new-section
touch new-section/index.qmd

Deployment

# Automatic deployment via GitHub Actions on push to master
git add .
git commit -m "Add new content"
git push origin master

Project Structure

_quarto.yml - Main configuration file with site settings, navigation, and formatting
index.qmd - Homepage with automatic post listings
about.qmd - About page content
posts/ - Blog posts organized by year:
- 2018/ - 3 posts (Stockholm weather, reminder bot, self-portrait)
- 2019/ - 2 posts (readability TED, r-bloggers)
- 2020/ - 5 posts (kinfitr series, nonlinear modeling, text API)
- index.qmd - Posts listing page with search and filtering
projects/ - Projects section (expandable for case studies)
papers/ - Academic papers section with publications list
images/ - Static images and assets
styles.css - Custom CSS styling for improved appearance
custom.scss - SCSS theme customization
.github/workflows/ - GitHub Actions deployment pipeline

Content Creation

Blog Posts

Create .qmd file in posts/YYYY/ directory
Add YAML frontmatter:

---
title: "Post Title"
author: "Granville Matheson"
date: "YYYY-MM-DD"
categories: ["Blog"]
tags: [R, Data Science]
description: "Brief description"
---

Write content using Quarto markdown
Preview locally, commit, and push

New Sections

Create directory with index.qmd
Update _quarto.yml navbar configuration
Test navigation and deployment

Key Features

Math rendering: Uses KaTeX for LaTeX math
Code highlighting: Syntax highlighting for R and other languages
R code execution: Can execute R chunks during rendering
Search: Built-in site search functionality
Comments: Disqus integration for post comments
Analytics: Google Analytics tracking
RSS: Automatically generated feeds

Deployment Architecture

GitHub Actions workflow renders site automatically
GitHub Pages hosts the static site
R dependencies installed via GitHub Actions
Quarto handles rendering and optimization

Migration Notes (2024)

This blog was successfully migrated from Hugo/blogdown to Quarto to resolve: - Broken math rendering - Now uses KaTeX for reliable LaTeX math display - Missing R code syntax highlighting - Restored with proper themes and colors
- Outdated dependencies - Hugo/blogdown toolchain was breaking with updates - Complex deployment - Simplified with GitHub Actions automation

Migration preserved: - All 13 original blog posts (10 .Rmd + 3 .md files) - Publication list and about page content - Site structure and URLs for SEO - Disqus comments and Google Analytics integration

Troubleshooting

Build failures: Check GitHub Actions logs in repository Actions tab
Syntax errors: Use quarto check for validation
Rendering issues: Clear cache with quarto render --cache-refresh
Missing R packages: Add to .github/workflows/quarto-publish.yml dependencies
Math not displaying: Ensure using $$ for display math, $ for inline
Code highlighting broken: Check language specification in code blocks

Important Instructions

NEVER add eval=FALSE to any R code chunks in this repository - all code should execute properly with the correct dependencies installed

# CLAUDE.md This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository. ## Repository Overview This is a Quarto-based blog focused on data science, pharmacokinetic modeling, and R tutorials, authored by Granville Matheson. It was successfully migrated from Hugo/blogdown to Quarto in 2024 to fix rendering issues and modernize the tech stack. ## Development Environment - **Quarto**: Primary static site generator - **R**: For executing code in posts and data analysis - **GitHub Actions**: Automated deployment pipeline ## Common Commands ### Local Development ```bash # Preview the site locally with live reload quarto preview # Render the entire site quarto render # Check for issues quarto check # Clear cache if having rendering issues quarto render --cache-refresh ``` ### Content Management ```bash # Add new post (create in appropriate year directory) mkdir -p posts/2024 touch posts/2024/new-post.qmd # Add new section mkdir new-section touch new-section/index.qmd ``` ### Deployment ```bash # Automatic deployment via GitHub Actions on push to master git add . git commit -m "Add new content" git push origin master ``` ## Project Structure - `_quarto.yml` - Main configuration file with site settings, navigation, and formatting - `index.qmd` - Homepage with automatic post listings - `about.qmd` - About page content - `posts/` - Blog posts organized by year: - `2018/` - 3 posts (Stockholm weather, reminder bot, self-portrait) - `2019/` - 2 posts (readability TED, r-bloggers) - `2020/` - 5 posts (kinfitr series, nonlinear modeling, text API) - `index.qmd` - Posts listing page with search and filtering - `projects/` - Projects section (expandable for case studies) - `papers/` - Academic papers section with publications list - `images/` - Static images and assets - `styles.css` - Custom CSS styling for improved appearance - `custom.scss` - SCSS theme customization - `.github/workflows/` - GitHub Actions deployment pipeline ## Content Creation ### Blog Posts 1. Create `.qmd` file in `posts/YYYY/` directory 2. Add YAML frontmatter: ```yaml --- title: "Post Title" author: "Granville Matheson" date: "YYYY-MM-DD" categories: ["Blog"] tags: [R, Data Science] description: "Brief description" --- ``` 3. Write content using Quarto markdown 4. Preview locally, commit, and push ### New Sections 1. Create directory with `index.qmd` 2. Update `_quarto.yml` navbar configuration 3. Test navigation and deployment ## Key Features - **Math rendering**: Uses KaTeX for LaTeX math - **Code highlighting**: Syntax highlighting for R and other languages - **R code execution**: Can execute R chunks during rendering - **Search**: Built-in site search functionality - **Comments**: Disqus integration for post comments - **Analytics**: Google Analytics tracking - **RSS**: Automatically generated feeds ## Deployment Architecture - **GitHub Actions** workflow renders site automatically - **GitHub Pages** hosts the static site - **R dependencies** installed via GitHub Actions - **Quarto** handles rendering and optimization ## Migration Notes (2024) This blog was successfully migrated from Hugo/blogdown to Quarto to resolve: - **Broken math rendering** - Now uses KaTeX for reliable LaTeX math display - **Missing R code syntax highlighting** - Restored with proper themes and colors - **Outdated dependencies** - Hugo/blogdown toolchain was breaking with updates - **Complex deployment** - Simplified with GitHub Actions automation **Migration preserved:** - All 13 original blog posts (10 .Rmd + 3 .md files) - Publication list and about page content - Site structure and URLs for SEO - Disqus comments and Google Analytics integration ## Troubleshooting - **Build failures**: Check GitHub Actions logs in repository Actions tab - **Syntax errors**: Use `quarto check` for validation - **Rendering issues**: Clear cache with `quarto render --cache-refresh` - **Missing R packages**: Add to `.github/workflows/quarto-publish.yml` dependencies - **Math not displaying**: Ensure using `$$` for display math, `$` for inline - **Code highlighting broken**: Check language specification in code blocks ## Important Instructions - NEVER add eval=FALSE to any R code chunks in this repository - all code should execute properly with the correct dependencies installed