yaml header

At a minimum, any R markdown file must tell R studio what sort of file should be created (.html, .docx, or .pdf). This information is included right at the top of the .Rmd file, in a header that contains yaml script (YAML = Yet Another Markup Language²).

Thus the minimum yaml header would appear as such:

---
output: word_document
---

Here is the yaml header for the homework template:

---
title: "Assignment title"
author: "your name goes here"
date: '03 September 2020'
output: word_document
---

A lot of customization can be fed via the yaml header. Here’s the header for the write-up on my research on fracking in South Africa:

---
title: Local perceptions of hydraulic fracturing ahead of exploratory drilling in eastern South Africa 
author: |
  | Devan Allen McGranahan $*$ & Kevin P. Kirkman $**$ 
  |
  | $*$ North Dakota State University, Fargo, ND USA
  | $**$ University of KwaZulu-Natal, Pietermaritzburg
  |
date: |
  | Version date: 03 September 2020
output: 
   tufte::tufte_html:
    tufte_variant: "envisioned"
header-includes:
  - \renewcommand{\themarginnote}{\roman{footnote}}
bibliography: KZN_fracking.bib
link-citations: no
csl: superscripted.csl
---

Code chunks

For R studio et al.³ to know you want some \({\bf\textsf{R}}\) script chugged, you need to identify the script as such. This is what’s called a code chunk and absolutely must have the following setup:

```{r}

```

• Both sets of triple backticks must be flush to the left. On most keyboards, the backtick is above Tab, to the left of 1.
• The {r} is what identifies it as an \({\bf\textsf{R}}\) code chunk.

All other text outside of the code chunk appears in the final document just like these words here–as regular old text.

Note that some operands have different meanings inside vs. outside code chunks. For example, in a code chunk, # is a comment and will be ignored when the \({\bf\textsf{R}}\) script is chugged; outside of a code chunk, # is the Markdown shortcut for a top-level section heading,⁴ followed by ## and ### as sub-section and sub-subsection, respectively.

Important

If you need to use a function from a package in a code chunk, be sure to include script for loading the package in the R markdown file, even if you have it loaded in the session. R markdown files are like self-contained \({\bf\textsf{R}}\) sessions, so it only knows what you tell it.

Chunk options

There are a lot of options one can add to the code chunk to fine-tune its behavior and output. At this point, you really don’t need to wory about any of them. Eventually, you will need to know how to use at least two:

• echo= specifies whether the script in the chunk will appear in the document (TRUE) or not (FALSE). For the first half of the course, always set echo = TRUE so we can see the script used to create a graph, etc. But you wouldn’t do this for your thesis or paper (yes, you can create both in R Markdown). Later on, we will set echo = FALSE and learn how to combine all the script together in an appendix at the end of the document.

• eval= determines whether to chug (TRUE) or ignore (FALSE) the script. Use eval=FALSE when you want to demonstrate how to make a graph, say, but not produce output:

```{r eval = FALSE}
plot(1:10)
```

Two others that are handy include fig.height= and fig.width= for adjusting the size of your figures, which helps prevent axis labels from getting cut off, etc.