15 Bookdown: Quick Start

15.1 ⭐️Overview

Document the process of creating a bookdown book. Think of it as a quick start guide.

Complete documentation at: https://bookdown.org/yihui/bookdown/

15.2 🌎Useful websites

15.3 Creating the bookdown project locally

  1. Start by clicking New Project -> New Directory -> Book project using Bookdown.

  2. Add a NOTES file and add it to .gitignore and .Rbuildignore using usethis:

    • usethis::use_build_ignore("NOTES")
    • usethis::use_git_ignore("NOTES")

  3. Delete all Rmd files except index.Rmd

  4. Create a folder named chapters.

  5. Edit the README file. It can say whatever you want it to. For examples, see here:

  6. Add a license file to the project’s root directory. Here is an example.

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/4.0/ or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.

15.4 Initiate a git repository

You need to do this in order to connect to GitHub, and you need to connect to GitHub before editing some of the books configuration files because you will need to add links to the repository.

  1. Type “usethis::use_git(message =”Initial commit”)” in the R console.

15.5 Create a github repository for the book

  1. Go to: https://github.com/orgs/brad-cannell/dashboard

  2. Click New

  3. Name the repository. For example, “r_notes”

  4. Optionally, type in a description. For example, “This is the repository for my R notes bookdown project.”

  5. Make the repository public

  6. Don’t check the boxes for README, .gitignore, or license

  7. Click create repository

  8. Follow GitHub’s instructions for pushing the repository to GitHub.

At this point, the GitHub repository should be set up.

15.6 Configuring a publishing source for the GitHub Pages site

Useful websites:
* https://bookdown.org/yihui/bookdown/github.html
* https://docs.github.com/en/pages/getting-started-with-github-pages/configuring-a-publishing-source-for-your-github-pages-site

  1. In the repository, click on Settings, then pages (on the left sidebar).

  2. Change the source to Branch:master, folder = docs

15.7 Modify _bookdown.yml

Start with this example and modify as needed

book_filename: "R 4 Epidemiology"
repo: https://github.com/brad-cannell/r4epi
output_dir: docs
delete_merged_file: true
language:
  ui:
    chapter_name: ""
new_session: no
rmd_subdir: ["chapters"]

15.8 Modify _output.yml

Start with this example and modify as needed

bookdown::gitbook:
  css: style.css
  config:
    toc:
      collapse: section
      scroll_highlight: yes
      before: |
        <li><a href="./">R for Epidemiology</a></li>
      after: |
        <li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>

15.9 Modify style.css

/******************************************************************************
CSS for the R4Epi textbook
******************************************************************************/

/*
CSS that came with bookdown
*/
p.caption {
  color: #777;
  margin-top: 10px;
}
p code {
  white-space: inherit;
}
pre {
  word-break: normal;
  word-wrap: normal;
}
pre code {
  white-space: inherit;
}

/* 
Font Styles
*/
.large-bold {
  font-size: 2em;
  font-weight: bold;
}

.underline {
  text-decoration: underline;
}

.red-text {
  color: red;
}

.code {
  color: #0365C0;
  font-family: "Courier New", Courier, monospace;
}


/*
Note styles
*/
.note {
  -moz-border-radius: 6px;
  -webkit-border-radius: 6px;
  background-color: #f0f7fb;
  border: solid 1px #3498db;
  border-radius: 6px;
  line-height: 18px;
  overflow: hidden;
  padding: 15px 15px;
}

.warning {
  -moz-border-radius: 6px;
  -webkit-border-radius: 6px;
  background-color: #FEFBEA;
  border: solid 1px #F2E394;
  border-radius: 6px;
  line-height: 18px;
  overflow: hidden;
  padding: 15px 15px;
}

15.10 Modify index.Rmd

  1. Delete all the example text.

  2. Modify the YAML header. Here is an example:

--- 
title: "R for Epidemiology"
author: "Brad Cannell"
date: "2024-05-31"
site: bookdown::bookdown_site
documentclass: book
bibliography: [book.bib, packages.bib]
link-citations: yes
csl: ama.csl
github-repo: brad-cannell/r4epi
url: 'https://brad-cannell.github.io/r4epi/'
description: "This is the textbook for Brad Cannell's Introduction to R Programming for Epidemiologic Research course."
---

  • The csl: ama.csl part of the YAML header allows you to change the bibliography style. You can find a list of styles here: https://github.com/citation-style-language/styles

  • For AMA, which I frequently want, you can just copy and paste from your templates folder.

  1. First-level headers become chapters. Use {-} at the end of the header if you don’t want the chapter to be numbered. For example # Welcome {-}

15.11 Creating bookdown chapters

Each Rmd file is a chapter. Chapters can be broken up into parts. To do so, create a subdirectory for each part inside the chapters folder. The individual Rmd files (i.e. chapters) go inside these folders.

I typically prefix each folder name that aligns with the order the parts should appear in. For example 01_getting_started, 02_best_practices, etc.

The first Rmd file in each part folder should have only this content:

# (PART) Getting Started {-}

<!-- This Rmd just creates a part heading in the table of contents -->

Name the file 00_part_<part_name>

All subsequent content chapters should start with a first level heading only – No YAML. For example, # R scripts.

For more on chapter content, see Bookdown template chapter

15.12 Knitting the book

  1. Click on the build tab, then click “Build Book”.

  2. Commit the changes and push to GitHub.

  3. After a few minutes, you should see the GitHub pages version working.

15.13 Errors and warnings

Output created: docs/index.html Warning message: In split_chapters(output, gitbook_page, number_sections, split_by, : You have 3 Rmd input file(s) but only 2 first-level heading(s). Did you forget first-level headings in certain Rmd files?

Solution: Just ignore this.

tlmgr: Local TeX Live (2019) is older than remote repository (2020).

Solution: Run tinytex::reinstall_tinytex()

! sh: xelatex: command not found

You might get this error when trying to build a book in pdf format.

Solution: Install MacTEX: https://www.tug.org/mactex/

! LaTeX Error: Cannot determine size of graphic in img/getting_started/01_install_r/download_r_mac.gif (no BoundingBox).

Solution: This is from trying to make a pdf document with a gif in it. LaTeX doesn’t support gifs. Just make a just build the book in gitbook format.

2: The label(s) fig:source1 not found.

Solution: Figures must have a caption in order to cross reference them.

[WARNING] Citeproc: citation examples not found

Solution: I haven’t found a solution yet, but so far the warning seems ignorable.