Pkgdown Website

name: pkgdown-website description: Build and deploy professional package documentation websites using pkgdown with Bootstrap 5, GitHub Pages, and automated workflows

pkgdown Website Development

This skill covers creating comprehensive, professional package documentation websites using pkgdown with Bootstrap 5 theming, GitHub Pages deployment, and automated CI/CD workflows.

Rules

1. Always use Bootstrap 5 with modern theming capabilities including dark mode
2. URLs must match across DESCRIPTION, _pkgdown.yml, and GitHub Pages settings
3. Use GitHub Actions for automated deployment (don't build locally and commit)
4. Organize documentation with clear reference sections and article groupings
5. Enable dark mode using light-switch theme for better user experience
6. Include social links in navbar for package promotion and author contact
7. Math rendering should use KaTeX for fast, client-side rendering
8. Custom fonts via Google Fonts improve branding and readability
9. Development mode should be set to auto for version-appropriate messaging
10. Test locally with pkgdown::build_site() before deploying

Complete _pkgdown.yml Configuration

Full Template with All Features

url: https://username.github.io/packagename/
template:
  bootstrap: 5
  theme: arrow-light
  bslib:
    base_font: {google: "Atkinson Hyperlegible"}
    heading_font: {google: "Fraunces"}
    code_font: {google: "JetBrains Mono"}
    bg: "#ffffff"
    fg: "#1e1e1e"
    primary: "#0054AD"
    secondary: "#767676"
  light-switch: true
  math-rendering: katex

development:
  mode: auto
  version_label: danger
  version_tooltip: "Development version"

home:
  title: "packagename: An Amazing R Package"
  description: >
    A comprehensive toolkit for doing amazing things in R.
    This package provides intuitive functions and robust workflows.
  links:
  - text: Ask a question
    href: https://github.com/username/packagename/discussions
  - text: Report a bug
    href: https://github.com/username/packagename/issues

authors:
  Your Name:
    href: https://yourwebsite.com
  Another Author:
    href: https://github.com/anotherusername

navbar:
  structure:
    left:  [home, intro, reference, articles, news]
    right: [search, github, linkedin, twitter]
  components:
    home:
      icon: fas fa-home fa-lg
      href: index.html
      aria-label: Home
    intro:
      text: Get started
      href: articles/packagename.html
    reference:
      text: Reference
      href: reference/index.html
    articles:
      text: Articles
      menu:
      - text: "Getting Started"
        href: articles/packagename.html
      - text: "Advanced Usage"
        href: articles/advanced-usage.html
      - text: "Examples"
        href: articles/examples.html
      - text: -------
      - text: "All Articles"
        href: articles/index.html
    news:
      text: News
      href: news/index.html
    github:
      icon: fab fa-github fa-lg
      href: https://github.com/username/packagename
      aria-label: GitHub
    linkedin:
      icon: fab fa-linkedin fa-lg
      href: https://www.linkedin.com/in/yourprofile/
      aria-label: LinkedIn
    twitter:
      icon: fab fa-twitter fa-lg
      href: https://twitter.com/yourhandle
      aria-label: Twitter

reference:
  - title: "Data Import and Export"
    desc: >
      Functions for reading and writing data files in various formats.
    contents:
      - read_data
      - write_data
      - import_csv
      - export_excel

  - title: "Data Manipulation"
    desc: >
      Core functions for transforming and cleaning data.
    contents:
      - clean_data
      - transform_variables
      - filter_rows
      - select_columns

  - title: "Statistical Analysis"
    desc: >
      Functions for statistical modeling and hypothesis testing.
    contents:
      - fit_model
      - test_hypothesis
      - calculate_statistics
      - generate_report

  - title: "Visualization"
    desc: >
      Create publication-quality plots and charts.
    contents:
      - plot_distribution
      - create_scatter
      - visualize_trends
      - export_plot

  - title: "Utilities"
    desc: >
      Helper functions and package configuration.
    contents:
      - validate_input
      - check_dependencies
      - packagename_options
      - print.packagename_object

  - title: "Internal Functions"
    desc: >
      Internal functions not intended for direct use.
    contents:
      - has_keyword("internal")

articles:
  - title: "Tutorials"
    navbar: Tutorials
    contents:
      - packagename
      - getting-started
      - basic-workflow

  - title: "Advanced Topics"
    navbar: Advanced
    contents:
      - advanced-usage
      - performance-optimization
      - extending-packagename

  - title: "Case Studies"
    navbar: ~
    contents:
      - case-study-1
      - case-study-2
      - real-world-examples

footer:
  structure:
    left: developed_by
    right: built_with
  components:
    developed_by: "Developed by [Your Name](https://yourwebsite.com)"
    built_with: "Built with [pkgdown](https://pkgdown.r-lib.org/) and [Bootstrap 5](https://getbootstrap.com/)"

Minimal _pkgdown.yml Template

url: https://username.github.io/packagename/
template:
  bootstrap: 5
  light-switch: true

development:
  mode: auto

DESCRIPTION File URL Configuration

The URL field in DESCRIPTION must match _pkgdown.yml:

Package: packagename
Title: An Amazing R Package
Version: 0.1.0
URL: https://username.github.io/packagename/, https://github.com/username/packagename
BugReports: https://github.com/username/packagename/issues

Note: Multiple URLs are comma-separated. Package website comes first, then GitHub repo.

Initial Setup with usethis

Complete Setup Process

# 1. Initialize pkgdown structure
usethis::use_pkgdown()

# 2. Configure for GitHub Pages (recommended)
usethis::use_pkgdown_github_pages()

# This function:
# - Adds URL to DESCRIPTION
# - Creates _pkgdown.yml
# - Adds GitHub Actions workflow
# - Configures .gitignore for docs/
# - Sets up gh-pages branch

Manual Setup (if needed)

# Create basic structure
usethis::use_pkgdown()

# Build site locally
pkgdown::build_site()

# Preview in browser
pkgdown::preview_site()

# Build specific components
pkgdown::build_reference()
pkgdown::build_articles()
pkgdown::build_home()
pkgdown::build_news()

GitHub Actions Workflow

Complete pkgdown.yaml Workflow

Create .github/workflows/pkgdown.yaml:

# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]
  release:
    types: [published]
  workflow_dispatch:

name: pkgdown

# Only allow one deployment at a time
concurrency:
  group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}

permissions:
  contents: write

jobs:
  pkgdown:
    runs-on: ubuntu-latest
    # Only restrict concurrency for non-PR jobs
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Setup Pandoc
        uses: r-lib/actions/setup-pandoc@v2

      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - name: Install dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::pkgdown, local::.
          needs: website

      - name: Build site
        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
        shell: Rscript {0}

      - name: Deploy to GitHub Pages
        if: github.event_name != 'pull_request'
        uses: JamesIves/github-pages-deploy-action@v4
        with:
          folder: docs
          branch: gh-pages
          clean: true

Alternative: Simple Deployment Workflow

on:
  push:
    branches: [main]

name: pkgdown

permissions:
  contents: write

jobs:
  pkgdown:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    steps:
      - uses: actions/checkout@v4
      - uses: r-lib/actions/setup-pandoc@v2
      - uses: r-lib/actions/setup-r@v2
      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::pkgdown, local::.
          needs: website
      - name: Build and deploy
        run: |
          pkgdown::deploy_to_branch(new_process = FALSE)
        shell: Rscript {0}

Bootstrap 5 Theming

Built-in Themes

pkgdown includes several Bootstrap 5 themes:

• arrow-light / arrow-dark (Tidyverse theme)
• Standard Bootstrap 5 themes

template:
  bootstrap: 5
  theme: arrow-light  # or arrow-dark

Custom Color Scheme with bslib

template:
  bootstrap: 5
  bslib:
    # Base colors
    bg: "#ffffff"           # Background
    fg: "#212529"           # Foreground text
    primary: "#0054AD"      # Primary brand color
    secondary: "#6c757d"    # Secondary color
    success: "#198754"
    info: "#0dcaf0"
    warning: "#ffc107"
    danger: "#dc3545"

    # Typography
    base_font: {google: "Roboto"}
    heading_font: {google: "Roboto Slab"}
    code_font: {google: "Fira Code"}
    font_scale: 1.0

    # Spacing
    spacer: 1rem

Google Fonts Options

Popular font combinations:

# Professional
bslib:
  base_font: {google: "Atkinson Hyperlegible"}
  heading_font: {google: "Fraunces"}
  code_font: {google: "JetBrains Mono"}

# Modern
bslib:
  base_font: {google: "Inter"}
  heading_font: {google: "Inter"}
  code_font: {google: "Fira Code"}

# Classic
bslib:
  base_font: {google: "Lato"}
  heading_font: {google: "Merriweather"}
  code_font: {google: "Source Code Pro"}

# Friendly
bslib:
  base_font: {google: "Nunito"}
  heading_font: {google: "Nunito"}
  code_font: {google: "Ubuntu Mono"}

Reference Organization

Grouping Functions by Purpose

reference:
  - title: "Core Functions"
    desc: "Main user-facing functions"
    contents:
      - has_concept("core")

  - title: "Data Processing"
    contents:
      - starts_with("process_")
      - starts_with("transform_")

  - title: "Plotting Functions"
    contents:
      - matches("plot|visualize|graph")

  - title: "S3 Methods"
    contents:
      - matches("\\.")

  - title: "Datasets"
    desc: "Example datasets included with the package"
    contents:
      - has_keyword("datasets")

Using Roxygen Concepts

In your function documentation:

#' @concept core
#' @concept data-import

Then in _pkgdown.yml:

reference:
  - title: "Core Functions"
    contents:
      - has_concept("core")
  - title: "Data Import"
    contents:
      - has_concept("data-import")

Articles Configuration

Organizing Vignettes

articles:
  - title: "Getting Started"
    navbar: "Get Started"
    desc: "New to the package? Start here!"
    contents:
      - introduction
      - installation
      - quick-start

  - title: "Workflows"
    navbar: "Workflows"
    contents:
      - basic-workflow
      - advanced-workflow
      - batch-processing

  - title: "Reference"
    navbar: ~  # Don't show in navbar
    contents:
      - technical-details
      - algorithm-description

Common Pitfalls

1. URL Mismatch

Problem: Website deploys but links are broken

Solution: Ensure URLs match exactly in three places:

# DESCRIPTION
URL: https://username.github.io/packagename/

# _pkgdown.yml
url: https://username.github.io/packagename/

# GitHub Settings > Pages
Source: gh-pages branch, / (root)

Note: Trailing slash matters! Be consistent.

2. GitHub Pages Not Enabling

Problem: Workflow runs but site doesn't appear

Solution:

1. Check GitHub repo Settings > Pages
2. Source should be "Deploy from a branch"
3. Branch should be "gh-pages" and "/ (root)"
4. Wait 2-3 minutes after first deployment
5. Check https://username.github.io/packagename/

3. Missing Dependencies

Problem: Build fails with "package not found"

Solution: Add to DESCRIPTION:

Suggests:
    pkgdown,
    knitr,
    rmarkdown

4. Math Not Rendering

Problem: LaTeX equations show as raw code

Solution: Enable math rendering:

template:
  math-rendering: katex  # or mathjax

In your .Rmd:

Inline: $E = mc^2$
Display: $$\int_0^\infty e^{-x^2} dx = \frac{\sqrt{\pi}}{2}$$

5. Icons Not Showing

Problem: Social media icons appear as text

Solution: Use FontAwesome classes correctly:

navbar:
  components:
    github:
      icon: fab fa-github fa-lg  # fab for brands
      href: https://github.com/user/repo
    home:
      icon: fas fa-home fa-lg    # fas for solid
      href: index.html

6. Dark Mode Issues

Problem: Dark mode has poor contrast

Solution: Test both modes and adjust:

template:
  light-switch: true
  bslib:
    # Light mode
    bg: "#ffffff"
    fg: "#212529"
    # These will auto-adjust for dark mode
    # Or specify dark mode explicitly

7. Development Version Badge

Problem: Release version shows "dev" badge

Solution: Use automatic mode:

development:
  mode: auto  # auto-detects based on version number

Version numbering:

• Development: 0.1.0.9000
• Release: 0.1.0

8. Large Site Build Time

Problem: Build takes >10 minutes on GitHub Actions

Solution:

# In workflow, use cached dependencies
- uses: r-lib/actions/setup-r-dependencies@v2
  with:
    extra-packages: any::pkgdown, local::.
    needs: website

# In _pkgdown.yml, skip heavy computations
template:
  params:
    docsearch:
      api_key: YOUR_KEY
      index_name: YOUR_INDEX

9. Broken Internal Links

Problem: Links between articles don't work

Solution: Use relative paths:

See the [advanced tutorial](advanced-usage.html) for more.
See [function reference](../reference/my_function.html).

10. Custom CSS Not Applied

Problem: Custom styles don't appear

Solution:

template:
  includes:
    in_header: |
      <link rel="stylesheet" href="custom.css">

Create pkgdown/extra.css (automatically included):

.navbar {
  background-color: #0054AD !important;
}

Testing and Validation

Local Testing

# Full site build
pkgdown::build_site()

# Individual components
pkgdown::build_reference()
pkgdown::build_home()
pkgdown::build_articles()
pkgdown::build_news()

# Preview in browser
pkgdown::preview_site()

# Clean and rebuild
pkgdown::clean_site()
pkgdown::build_site()

Validation Checklist

• All URLs match (DESCRIPTION, _pkgdown.yml, GitHub)
• Site builds without errors locally
• All reference pages render correctly
• Articles render with proper formatting
• Links between pages work
• Dark mode has good contrast
• Icons display properly
• Math equations render (if applicable)
• Code examples run correctly
• Mobile view is responsive
• Search functionality works
• Social links point to correct profiles

Advanced Features

Search Integration

Algolia DocSearch (free for open source):

template:
  params:
    docsearch:
      api_key: YOUR_API_KEY
      index_name: YOUR_INDEX_NAME

Custom Footer

footer:
  structure:
    left: [developed_by, citation]
    right: [built_with, legal]
  components:
    developed_by: "Developed by [Your Name](https://yoursite.com)"
    citation: "Please cite this package as..."
    built_with: "Built with pkgdown"
    legal: "[Privacy Policy](privacy.html) | [Terms](terms.html)"

OpenGraph and Twitter Cards

home:
  opengraph:
    image:
      src: man/figures/card.png
      alt: "Package logo"
    twitter:
      creator: "@yourhandle"
      card: summary_large_image

This creates rich previews when shared on social media.

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