---
title: My Thesis
author: You
output: html_document
---

## The Title and YAML Header

The top of the RMarkdown document contains *metadata* about the document itself.  The `yaml` header tells RStudio (and [Pandoc](https://pandoc.org/)) how to actually compile the document, and what kinds of information it may need.  There are different kinds of output, including `html_document`, `html_notebook`, `word_document`, and others.  You can see a list of options on the [RStudio RMarkdown page](https://rmarkdown.rstudio.com/lesson-9.html).  

## Knitting your Thesis

Open this `Rmd` file in RMarkdown. It should all be ready to go, to turn it into a cool `HTML` document. To do that, look at the RStudio toolbar and click the `knit` button.

You can also knit (or render) your RMarkdown documents using the command line. There are good reasons for doing this, and cool tricks you can try (see the Tips & Tricks later in the workshop). To do that, go to the folder that your RMarkdown document is in and type in the command:

```
Rscript -e "rmarkdown::render('filename.Rmd')"
```

No need to try it here, but just wanted to mention it :)

## Document Templates

Most universities and departments make a Word or latex template available for theses. For example, the [template in the `templates` folder](templates/thesistemplate.docx) is provided by [Simon Fraser University](https://www.lib.sfu.ca/help/publish/thesis/templates).

## Bibliography

Pandoc (and by extension, RMarkdown) can support the use of a bibliography in [Bibtex format](http://www.bibtex.org/). These references can be rendered into a number of different formats using an XML-type file called the [Citation Style Language](https://citationstyles.org/), or CSL. These files define how the reference is rendered and referenced in text. You can see a full list of available formats (for a large number of journals) in the [CSL Github styles repository](https://github.com/citation-style-language/styles).

If I wanted to cite a paper, for example, the winner of an IgNobel prize for making feces knives `[@eren2019experimental]`, I could simply add an in text citation to my bibliography file. We'll edit this further once we get used to using `git` workflows.

There's some great information about [using RMarkdown citations & bibliographies](https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html) on the RStudio website.