_output.yml

bookdown::gitbook:
  includes:
    in_header: addons/ga.html
  css: css/style.css
  split_by: section
  config:
    toc:
      collapse: none
      before: |
        <li><a href="./">Computational Genomics with R</a></li>
      after: |
        <li><a href="https://bookdown.org" target="_blank">Published with bookdown</a></li>
    download: [pdf]
    edit: https://github.com/compgenomr/book/edit/master/%s
    sharing:
      github: yes
      facebook: no
bookdown::html_chapters:
  css: [css/style.css, css/toc.css]
  fig_width: 6
  fig_height: 6
  fig_caption: true
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: "pdf"
  latex_engine: xelatex
  citation_package: natbib
  template: null
  pandoc_args: --top-level-division=chapter
  toc_depth: 3
  toc_unnumbered: no
  toc_appendix: yes
  fig_width: 5
  fig_height: 5
  fig_caption: true
  quote_footer: ["\\VA{", "}{}"]