Last but not least, we have the YAML header. Here is where you configure general settings for the final output file, and a few other things.

The settings are written in YAML format in the form key: value. Nested settings or sub-settings are indented with spaces. In the template R Markdown document you can see that html_document is nested under output, and in turn, toc is nested under html_document since it is a setting for the HTML output. The table of contents (TOC) is automatically compiled from the section headers (marked by #).

Add a subsection header somewhere in your document using three ###. Knit and look at how the table of contents is structured.
Now set toc: false and knit again. What happened?
A setting that works for HTML output is toc_float: true. Add that to your document (same indentation level as toc: true) and knit. What happened?
In the same way, add the option number_sections: true. What happened?
Do you think it looks weird with sections numbered with 0, e.g. 0.1? That is because the document does not contain any level-1-header. Add a header using only one # at the top of the document, just after the setup chunk. Knit and see what happens!

We can also set parameters in the YAML header. These are either character strings, numerical values, or logicals, and they can be used in the R code in the code chunks. Let’s try it out:

Add two parameters, data and color, to the YAML header. It should now look something like this:

---
title: "Untitled"
output:
    html_document:
        toc: true
        toc_float: true
        number_sections: true
params:
    data: cars
    color: blue
---

So now we have two parameters that we can use in the code! Modify the pressure code chunk so that it looks like this:

```{r pressure, fig.width = 6, fig.height = 4}
plot(get(params$data), col = params$color)
```

This will plot the dataset cars using the color blue, based on the parameters we set in the YAML header.

Knit and see what happens!

Later, we will learn how to set parameters using an external command.

We have up until now mainly been using html_document as an output format. There are however a range of different available formats to choose between. What is important to know, is that not all chunk settings work for all output formats (this mainly regards settings related to rendering plots and figures), and some YAML settings are specific for the given output format chosen.

Take a look at this gallery of R Markdown documents to see what different kinds of output formats are possible to generate.
Take a look at the last page of this reference for a list of YAML header options, and what output formats they are available for.

Quick recap
In this section you learned how to set document-wide settings in the YAML header, including document output type and user defined parameters.