4.1 bookdown project structure

Below shows the basic structure of a default bookdown project:

directory/
├──  index.Rmd
├── 01-intro.Rmd
├── 02-literature.Rmd
├── 03-method.Rmd
├── 04-application.Rmd
├── 05-summary.Rmd
├── 06-references.Rmd
├── _bookdown.yml
├── _output.yml
├──  book.bib
├──  preamble.tex
├──  README.md
└──  style.css

As a summary of these files:

  • index.Rmd: This is the only Rmd document to contain a YAML frontmatter, and is the first book chapter.

  • Rmd files: A typical bookdown book contains multiple chapters, and each chapter lives in one separate Rmd file.

  • _bookdown.yml: A configuration file for bookdown; includes book-specific metadata such as output directory, whether to create a new R session for each chapter.

  • _output.yml: It specifies the output formatting of the HTML, LaTeX/PDF, e-books, etc.

  • preamble.tex and style.css: They can be used to adjust the appearance and styles of the book output document(s). Knowledge of LaTeX and/or CSS is required.

These files are explained in greater detail in the following subsections.

_output.yml

_output.yml Output formats can be specified either

  • in the YAML metadata of the first Rmd file of the book (usually index.Rmd), or
  • in a separate YAML file named _output.yml under the root directory of the book.

See Section 12.4 in R Markdown: The Definitive Guide for a complete list of bookdown output formats. A quick takeaway is that bookdown supports both book types and single documents.

Common uses of _output.yml:

  • Specify supported output formats: bookdown::gitbook, bookdown::pdf_book, bookdown::epub_book, etc.

  • Add an edit link, e.g., https://github.com/my1396/R-Notes/edit/main/%s

    This will configure which remote repo to link to and hence allow the page to be downloadable as an .Rmd. Also need to specify download: ["rmd"].

  • Link to your GitHub in the toolbar (also need index.Rmd)

  • Add other sharing links

  • Header and footer of your TOC

  • Collapse the TOC by (sub)section

  • Code highlighting

    Here we use highlight: tango to apply the Tango theme.

    The issue is that Tango highlighting does not work well with dark mode.

Here is a brief example of _output.yml:

bookdown::gitbook:
  css: style.css
  highlight: tango
  split_by: section+number
  includes:
    in_header: head.html
  config:
    fontsettings:
      theme: sky
    toc:
      collapse: section
      before: |
        <li><a href="./">R Notes</a></li>
      after: |
        <li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
    toc_depth: 3
    edit: 
        link: https://github.com/my1396/R-Notes/edit/main/%s
    sharing:
        github: yes
    download: ["pdf", "epub", "rmd"]
    enableEmoji: true

bookdown::pdf_book:
  includes:
    in_header: preamble.tex
  latex_engine: xelatex
  citation_package: natbib
  keep_tex: yes

bookdown::epub_book: default

You do NOT need the three dashes --- in _output.yml. In this case, all formats should be at the top level, instead of under an output field in individual Rmds.

4.1.0.1 gitbook format

The output format bookdown::gitbook is built upon rmarkdown::html_document, which was explained in Section 3.1 in R Markdown: The Definitive Guide. The main difference between rendering in R Markdown and bookdown is that a book will generate multiple HTML pages by default.

bookdown::gitbook settings:

  • css: style.css specifies one or more custom CSS files to tweak the default CSS style.

    Note that bookdown::gitbook has a set of default CSS files. Use docs/libs/gitbook-2.6.7/css to see the default settings. If some of your custom CSS settings are not applied, it is likely due to conflicts with gitbook CSS. You may need to override the default CSS files by appending !important to your custom CSS settings.

  • There are several sub-options in the config option for you to tweak some details in the user interface. See here for the default settings of config.

    • Font/theme settings

      fontsettings:
# changing the default
  theme: night
  family: serif
  size: 3

      You can set the initial value of these settings via the fontsettings option.

      • Font size is measured on a scale of 0-4; the initial value can be set to 1, 2 (default), 3, or 4.
      • theme: white | sepia | night. Default to white.

    • toc option controls the behavior of the table of contents (TOC).

      You can collapse some items initially when a page is loaded via the collapse option. Its possible values are subsection (default), section, none (or null).

      collapse: section collapses the TOC at the level 1 headings, which keeps the appearance concise. This is useful when there are many chapters in the book.

      However, a side effect is that level 3 headings will never be expanded when navigating to a specific level 2 heading.

      • You need to click the level 2 heading in the TOC to expand it and see level 3 headings.

    • download: ["pdf", "epub", "rmd"] specifies which formats to allow users to download the book in.

      When download: null (by default), gitbook() will look for PDF, EPUB, and MOBI files in the book output directory, and automatically add them to the download option. If you just want to suppress the download button, use download: false.

  • split_by= c("chapter", "chapter+number", "section", "section+number", "rmd", "none") defaults to chapter, which splits the file by the first-level headers.

    • split_by: chapter splits the file by the first-level headers;

      A chapter page may be too long if there are many sections within chapters.

    • split_by: section splits the file by the second-level headers.

      • I prefer split_by: section+number as it orders all html in the book’s section order. ✅

    • split_by: chapter+number and section+number: the chapter/section numbers will be prepended to the HTML filenames. For example: if using chapter or section, the HTML file names will be introduction.html, literature.html, etc.; but with the numbering setting, the HTML file names will be 1-introduction.html, 2-literature.html, etc.

  • The includes option allows you to insert arbitrary custom content before and/or after the body of the output.

    It has three sub-options: in_header, before_body, and after_body. You need to know the basic structure of an HTML or LaTeX document to understand these options.

    • The source of an HTML document looks like this:
    <html>

  <head>
  <!-- head content here, e.g. CSS and JS -->
  </head>

  <body>
  <!-- body content here -->
  </body>

</html>

    The in_header option takes a file path and inserts it into the <head> tag. The before_body file will be inserted right below the opening <body> tag, and after_body is inserted before the closing tag </body>.

    Use example of includes option in HTML output.

    For example, when you have LaTeX math expressions rendered via the MathJax library in the HTML output, and want the equation numbers to be displayed on the left (default is on the right), you can create a text file (named mathjax-number.html) that contains the following code:

    <script type="text/x-mathjax-config">
MathJax.Hub.Config({
  TeX: { TagSide: "left" }
});
</script>

    Let’s assume the file mathjax-number.html is in the root directory of your book (the directory that contains all your Rmd files). You can insert this file into the HTML head via the in_header option, e.g.,

    ---
output:
  bookdown::gitbook:
    includes:
      in_header: mathjax-number.html
---

    Example of MathJax config files:

    Bookdown uses MathJax 2.7 by default.

    Define TeX macros

    You can include macro definitions in the Macros section of the TeX blocks of your configuration:

    MathJax.Hub.Config({
  TeX: {
    Macros: {
      RR: "{\\bf R}",
      bold: ["{\\bf #1}",1]
    }
  }
});

    Note that MathJax.Hub.Config is used in inline configuration. It is case-sensitive. Macros has capital M, and TeX, rather than tex, is used.

    • A LaTeX source document has a similar structure:
    \documentclass{book}

% LaTeX preamble
% insert in_header here

\begin{document}
% insert before_body here

% body content here

% insert after_body here
\end{document}

  • You can add a table of contents using the toc option and specify the depth of headers that it applies to using the toc_depth option.

    • If the TOC depth defaults to 3 in html_document.
    • For pdf_document, if the TOC depth is not explicitly specified, it defaults to 2 (meaning that all level 1 and 2 headers will be included in the TOC).
    ---
bookdown::gitbook:
    toc:
        collapse: subsection
    toc_depth: 3
---

    collapse specifies a level to expand to by default, aka at #, ##, or ###.

    I suggest collapsing at level 2. This way, you get a good overview of what each major topic (level 1 heading) includes, without showing the most detailed items.

    • collapse: subsection: At startup, the toc will collapse at the level 2 headings. As you go to one specific subsection, the content inside will expand. You can see level 3 headings. ✅
    • collapse: section: At startup, the toc will collapse at the level 1 headings, which keeps the appearance concise. However, a side effect is that level 3 headings will never be displaied when navigating to a specific level 2 heading.

bookdown 中文书籍 _output.yml 范例: https://github.com/yihui/bookdown-chinese/blob/96d526572f0c6648d06c2d4bebf57c5fb4eafce3/_output.yml

  • You can set up a tex template.

    Yihui sets up the Chinese support in the template file (latex/template.tex).

    bookdown::pdf_book:
  includes:
    in_header: latex/preamble.tex
    before_body: latex/before_body.tex
    after_body: latex/after_body.tex
  keep_tex: yes
  dev: "cairo_pdf"
  latex_engine: xelatex
  citation_package: natbib
  template: latex/template.tex

    The base format for bookdown::pdf_book is rmarkdown::pdf_document.

    dev: Graphics device to use for figure output, defaults to pdf.

_bookdown.yml

_bookdown.yml allows you to specify optional settings to build the book. For example:

  • Set output_dir: docs

  • Set new_session: yes

    When set to yes, it uses “Knit and Merge” (K–M), and creates a new R session for each chapter, which is useful for avoiding conflicts between packages or variables across chapters.

    The default is no, which uses “Merge and Knit” (M-K), where all chapters are knitted in one R session.

  • Change themes

  • Change the chapter name

  • Change chapter order

delete_merged_file: true
output_dir: "docs"
new_session: yes
language:
  ui:
    chapter_name: "Chapter "

Note that you don’t need to manually create the docs folder, bookdown will create one if it doesn’t exists.

  • delete_merged_file: whether to delete the main Rmd file after the book is successfully rendered. An Rmd file that is merged from all chapters; by default, it is named _main.Rmd.

  • before_chapter_script: one or multiple R scripts to be executed before each chapter.

  • After you serve your site locally, all supporting files will be output to docs. Be sure to add one .nojekyll file in docs to tell GitHub that your website is not to be built via Jekyll.

  • Because bookdown only overwrites existing files and does not delete unused ones, you can simply delete the docs folder so that bookdown will recreate everything necessary without any redundancy.

    Remember to recreate .nojekyll too after bookdown has created the new docs.

index.Rmd

index.Rmd homepage of your website. Contains the first chapter and the YAML metadata which will be applied to all other Rmd pages.

That is, index.Rmd sets the global YAML for the entire website. Moreover, index.Rmd is the only Rmd document that contains a YAML frontmatter.

See Chapter 2.2 in R Markdown: The Definitive Guide for YAML details.

Common uses of index.Rmd’s YAML frontmatter:

  • Book cover, title, author, date, and description

  • Add bibliography

    Once you have one or multiple .bib files, you may use the field bibliography in the YAML metadata of your first R Markdown document (which is typically index.Rmd), and you can also specify the bibliography style via biblio-style (this only applies to PDF output).

    bibliography: [book.bib, packages.bib]
biblio-style: "apalike"

    Add your user citation to book.bib in stead.

    Don’t remove packages.bib; it is automatically generated and overwritten every time you rebuild the book.

  • Link to your GitHub in the toolbar (also need _output.yml)

  • Add a favicon

    Add the following line to index.Rmd YAML:

    favicon: "images/r-project-favicon.ico"

    Issue: Favicon shows ok on Chrome but couldn’t display on Safari. Same issue reported in Stack Overflow.
    Fix: There is a delay for Safari to show Favicon. Wait for two hours and the issue resolves itself…

An example of index.Rmd

---
title: "A Minimal bookdown Project"
site: bookdown::bookdown_site
documentclass: book
bibliography: [book.bib, packages.bib]
csl: chicago-fullnote-bibliography.csl
github-repo: my1396/R-Notes
favicon: "images/r-project-favicon.ico"
# typesetting for LaTeX output
papersize: a4 # The printed size of the thesis
geometry:
  - top=25.4mm
  - bottom=25.4mm
  - left=25.4mm
  - right=38.1mm
  # - bindingoffset=6.4mm  # removes a specified space from the inner-side for twoside.
  # - asymmetric  # disable alternating margins on odd/even pages
classoption: 
  - twoside
  - openright
---

# Preface

Some content
  • site: bookdown::bookdown_site tells rmarkdown to use bookdown to build all Rmd files, instead of rendering a single Rmd file.

.Rmd files

  • Chapters (also sections) are based on separate Rmd files.

  • Besides index.Rmd, other R Markdown files will make up the chapters of your book. By default, bookdown merges all Rmd files by the order of filenames, e.g., 01-intro.Rmd will appear before 02-literature.Rmd.

  • The Rmd files must start immediately with the chapter title using the first-level heading, e.g., # Chapter Title. Note that YAML metadata should NOT be included in these Rmd files, as it is inherited from the index.Rmd file.

01-intro.Rmd

# Introduction

This chapter is an overview of the methods that
we propose to solve an **important problem**.

02-literature.Rmd

# Literature

Here is a review of existing methods.