File Structure and Headers

To understand our file structure, see the GitHub repository for this book at

In general, each subchapter is a separate .Rmd file.

Here is a simplified outline of the root file structure in the GitHub repo for this book:

  • Preface of the book with non-numbered sections: index.Rmd
  • Chapters with first-level headers in this format: 1-chapter.Rmd
  • Subchapters with second-level headers in this format: 1.1-subchapter.Rmd. While Bookdown refers to these as sections, we call them subchapters.
  • The images folder, where PNG, JPG, and PDF images to display in chapters are located.
  • The docs folder, which contains the published book products, such as Web edition (index.html, introduction.html, etc.), the PDF edition (Dougherty-etal-OnTheLine.pdf), etc.
  • Additional helper files described further below.

When you change the names of chapters/sections, Bookdown builds new HMTL pages based on those new names, but old HMTL pages based on old chapter/section names may still exist in the same subfolder. To avoid confusion, you may wish to carefully delete old HTML pages in docs whenever you significantly alter names and build a new version of the book.

Bookdown assigns a default ID to each header, which can be used for cross-references. The default ID for # Topic is {#topic}, and the default ID for ## Section Name is {#section-name}, where spaces are replaced by dashes. But we do not rely on default IDs because they might change due to editing or contain duplicates across the book.

Instead, we manually assign a unique ID to each first- and second-level header in the following way. Note that the {-} symbol, used alone or in combination with a space and a unique ID, prevents auto-numbering in the second- thru fourth-level headers:

# Top-level chapter title {#unique-name}
## Second-level section title {- #unique-name}
### Third-level subhead {-}
#### Fourth-level subhead {-}

Also, we match the unique ID keyword to the file name for top-level chapters this way: 01-keyword.Rmd to keep our work organized. Unique names should contain only alphanumeric characters (a-z, A-Z, 0-9) or dashes (-).

Subheaders must have unique names or IDs to avoid Bookdown errors about duplicated references.

In the Bookdown index.Rmd for the HTML book output and the PDF output, the toc_depth: 2 setting displays chapter and section headers down to the second level in the Table of Contents.

The split_by: section setting divides the HTML pages at the second-level header, which creates shorter web pages with reduced scrolling for readers. For each web page, the unique ID becomes the file name, and is stored in the docs subfolder.

The number_sections setting is true for the HTML and PDF editions, and given the toc_depth: 2, this means that they will display two-level chapter-section numbering (1.1, 1.2, etc.) in the Table of Contents. Note that number_sections must be true to display Figure and Table numbers in x.x format.

To override numbered sections in individual subchapters, insert a minus sign before the hashtag inside the curly brackets: ## Subchapter title {- #keyword}

See relevant settings in this excerpt from index.Rmd:

    toc_depth: 2
    split_by: section
    number_sections: true
    split_bib: true
  toc_depth: 2
  number_sections: true

Note that chapter and section numbering do not appear automatically in the MS Word output unless you supply a reference.docx file, as described in the RMarkdown guide and this Stack Overflow question.

In the _bookdown.yml settings, all book outputs are built into the docs subfolder of our GitHub repo, as shown in this excerpt:

output_dir: "docs"
delete_merged_file: true
book_filename: "OnTheLine"
    fig: "Figure "
    tab: "Table "
chapter_name: "Chapter "

In our GitHub repo, we set GitHub Pages to publish to the web using main/docs, which means that visitors can browse the source files at the root level, and view the HTML web pages hosted in the docs subfolder. We use the GitHub Pages custom domain setting so that the HTML edition is available at

The docs subfolder also may contain the following items, which are not generated by Bookdown and need to be manually created:

  • CNAME file for the custom domain, generated by GitHub Pages.
  • .nojekyll invisible empty file to ensure speedy processing of HTML files by GitHub Pages.
  • wp-content folder to redirect old links from the previous WordPress site at this domain
  • Note: Bookdown now generates a 404.html file that replaces the need for the custom version that previously needed to be manually created.

This HTML version of this book also includes the Google Analytics code file, and also a footer that appears at the bottom of each web page, with references in the index.Rmd code, as shown below.

      in_header: google-analytics-otl.html
      after_body: footer.html