Chapter 7 Nitty gritty stuff

In descending order of messiness (i.e., how confused I get)⁵

• Reference management + citations
• Notes to self within text
• Snippets! 💕
• Predefined functions
• Footnotes
• Cross-referencing sections/figs/tables
• Figure/table autonumbering
• Tables in RMarkdown
  • Specifically when working with both .docx and .pdf
• Appendices

7.1 Other resources

• Other Rmd + bookdown resources

7.2 Dissertating in Bookdown

7.2.1 Essential ingredients

• index.Rmd: Contains your YAML that will tell bookdown how to render your book
• .Rmd files that comprise the body of your book. These can be specific chapters, but can also be constructed modularly in whatever way you choose.
  • Unless specifically told otherwise, bookdown will compile these in alphanumeric order, so they should be named in the order you want them to appear.
    • In a nutshell, file names should be machine readable, human readable, and play well with default ordering (thank you, Jenny Bryan).

7.2.2 Non-essential but very helpful ingredients

• A .bib file contianing your references
• Separate directories containing your:
  • data (raw .csv files, etc)
  • scripts (helper .R scripts that contain the bulk work of your analyses)
  • images that are not created in R
• Template documents that will provide bookdown with the information it needs to style your document
  • Word: uwo_thesis_template.docx is a Word document containing the style settings required to output a Western-approved thesis. This template also contains text, but really all you need is a Word document with the style elements set that you wish to use
  • PDF: The tex folder contains two .tex files that use Latex to create a final PDF:
    • params.tex contains the Latex parameters required to compile the document
    • doc_preface.tex contains the front matter: everything that will appear before the beginning of the thesis

A note on the .tex documents: The documents provided here are comprised of a mash-up of two extremely useful resources:

• Lucy D’Agostino McGowan’s blogpost and dissertation toolkit provided the original versions of these documents and a super handy walkthrough on how to use them.
• Jon Clau’s updated Western .tex templates contain the information necessary to produce a Western U thesis (the files hosted on Western’s site are older versions)

7.2.3 Rendering the book

Once you have more than one .Rmd file, you are ready to render/compile them into a fully combined document.

The rendered version will appear in _book/

To render the book as whatever is listed as the default in index.Rmd, do:

bookdown::render_book("index.Rmd")

To render as a pdf or word document, do:

bookdown::render_book("index.Rmd", output_format = "pdf_book")
bookdown::render_book("index.Rmd", output_format = "word_document2")

A nice way to preview it is to render it as a gitbook:

bookdown::render_book("index.Rmd", "bookdown::gitbook")

Then open index.html in your browser, and run bookdown::serve_site() to update it whenever you save changes. This is much neater/navigable.

Beware of features that will only show up in pdf rendering (like certain features of kable, kableExtra), or that won’t compile for pdfs (like the emo package)

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5. Some of my confusion may be because I haven’t had to try hard to figure it out yet, and not necessarily related to the actual detail itself↩