CBW Bookdown Guide
I Introduction
1
CBW’s Bookdown Documentation
2
How Bookdown Works: A Primer
II Cheat Sheets
3
Editing Your Workshop
4
Handy Shortcuts
4.1
Getting to your folder in the terminal
4.2
Opening your folder from the terminal
4.3
Commenting and uncommenting in RStudio
5
FAQs
5.1
Why aren’t my changes appearing on the website?
5.2
What are the unusual symbols I’m seeing?
III Setup and Installations
6
Installations
7
Local Setup and SSH
7.1
SSH Connection
7.1.1
Generate an SSH key
7.1.2
Add your SSH key to the ssh-agent
7.1.3
Add your SSH key to your GitHub account
7.2
GitHub Folder
7.2.1
Create your folder
7.2.2
Clone the GitHub homepage
7.2.3
Clone the travel logistics repo
IV Set Up Workshop Site
8
Create your repo
8.1
Option 1: New repo
8.2
Option 2: Duplicate existing repo
9
Configure your repo
9.1
A note on repos vs websites
10
Deploy your site
10.1
Check your deploy and see your website!
A very specific build and deployment warning
11
Faculty team setup
12
Clone to your computer
12.1
Oops, I Git Cloned the Wrong Repository!
13
Finishing touches
14
Link to homepage
14.1
Get your code
14.2
Add to GitHub homepage
14.3
Add to GitHub sitemap
14.4
Update the website
15
Logistics page
15.1
Create your logistics page
16
What’s next?
16.1
Homepage
16.1.1
Pre-work
16.1.2
Schedule
16.1.3
Class photo
16.2
Faculty pages
16.3
Computing
16.4
Modules
16.4.1
Embedding slides
16.4.2
Embedding YouTube videos
16.4.3
Adding lab material
16.5
Bioschemas
16.6
What if I need to add a new file or change the existing file structure?
V Formatting
17
Markdown
17.1
Formatting your content
17.1.1
Option: Visual R Markdown
17.2
Chapters and subheaders
17.2.1
Sub-subheader
An unnumbered subheader
17.3
Parts
17.4
Text Formatting
Bold
Italics
Subscript
Superscript
Footnotes
Horizontal Line
Blockquote
Unordered List
Ordered List
Code
17.5
Links
External webpages
Other sections within your workshop website
17.6
Embedding
Images
PDFs
YouTube Videos
17.7
Citations
17.8
Equations
17.9
Theorems and Proofs
17.10
Using HTML
18
Callouts
18.1
Basic Syntax
18.2
Attribute Reference
18.3
Default Icons
18.4
Examples
18.4.1
Example 1: Informational Note
18.4.2
Example 2: Collapsible “Plain” Answer Box
18.4.3
Example 3: Important Red Warning
18.4.4
Example 4: Comprehensive Dropdown
18.5
Nesting Callouts
18.5.1
Example of a Nested Callout
19
Code
19.1
Rendering Code
19.2
Syntax highlighting
19.3
Running code
19.4
Code Chunk Options
19.5
Code Chunks for Code-Generated Figures and Tables
VI Reference Material
20
Command line crash course
20.1
Terminal, Command Prompt and Windows PowerShell
20.2
Common Commands (for us)
21
Bookdown crash course
21.1
How Bookdown works
21.2
File setup
_output.yml & _bookdown.yml
Organizing the TOC: .Rmd files
Folders
21.3
Working with your Bookdown project in RStudio
21.3.1
Opening your Bookdown project
21.4
Explaining RStudio
21.5
Build the Book
21.5.1
Other Ways to Build Your Book
21.5.2
Knit Your Book
21.5.3
Knit VS Build
21.5.4
Preview Your Book
21.6
Pushing to GitHub
Appendices
A
Appendix A: developers’ guide
A.1
GitHub Repo
A.2
Diagram Links
A.2.1
How to Publish a Google Drawing
B
Appendix B: homepage guide
B.1
Project Structure
B.2
How to Update Content
B.2.1
Add Your Image
B.2.2
Edit workshops.json
B.2.3
Example Entry:
B.3
Local Development & Validation
B.3.1
Live Validation in VS Code (Recommended)
B.3.2
Manual Validation via Command Line
B.4
Deployment
B.5
Common Debugging Steps
B.5.1
Symptom: The page is blank or workshops are not displaying.
B.5.2
Symptom: My recent changes are not appearing on the live site.
B.5.3
Symptom: A workshop card is showing a broken image.
C
References
Sponsors
CBW Bookdown Guide
C
References
Xie, Yihui. 2025.
Bookdown: Authoring Books and Technical Documents with r Markdown
.
https://github.com/rstudio/bookdown
.