_output.yml

bookdown::gitbook: # generating the gitbook (html) version of the thesis
  css: style.css
  author: Ladislas Nalborczyk
  date: "`r Sys.Date()`"
  github-repo: lnalborczyk/phd_thesis
  citation_package: none # natbib or biblatex - needs to be "none" in order to use the csl file
  pandoc_args: ["--csl", "./csl/apa6.csl"] # specifies the csl file to be used
  split_bib: false # if true, adds references at the end of each chapter
  # split_by: chapter # "none" creates only one html file
  config:
    toc:
      after: |
        <li><a href="https://github.com/rstudio/bookdown" target="blank"> Powered by bookdown </a></li>
        <li><a href="http://www.barelysignificant.com" target="blank"> Ladislas Nalborczyk </a></li>
      collapse: none # section / subsection
      scroll_highlight: yes
    edit: https://github.com/lnalborczyk/phd_thesis/edit/master/%s
    search: yes
    download: null # only pdf by default
    highlight: pygments

bookdown::pdf_book: # generating the pdf version of the thesis
  includes:
    in_header: latex/preamble.tex # defines style and latex options
    before_body: latex/before_body.tex # defines cover page
  latex_engine: xelatex # options are pdflatex, xelatex, or lualatex
  citation_package: none # natbib or biblatex - needs to be "none" (using pandoc-citeproc) in order to use the csl file
  keep_tex: true # keeps the .tex file
  toc_appendix: true # adds the appendix part to the table of contents
  dev: "cairo_pdf" # plotting device
  toc: false # deactivates default table of contents
  highlight: pygments # code highlighting style
  pandoc_args: ["--csl", "./csl/apa6.csl"] # specifies the .csl (citation style) file

# bookdown::word_document2: # generating the word version of the thesis
#   pandoc_args: [
#     "--csl", "./csl/apa6.csl",
#     "--bibliography", "./bib/packages.bib",
#     "--bibliography", "./bib/thesis.bib",
#     "--filter", "pandoc-citeproc"
#     ]