3.4 Rmd Basics

To name a chunk, add the name after r, it’s not necessary to add label='chunk-name', but it is possible to do so if you prefer the form tag=value.

The chunk label

Must be unique within the document. This is especially important for cache and plot filenames, because these filenames are based on chunk labels. Chunks without labels will be assigned labels like unnamed-chunk-i, where i is an incremental number.
Avoid spaces (␣), periods ( .), and underscores (_) in chunk labels and paths. If you need separators, you are recommended to use hyphens (-) instead.

knitr::opts_chunk$set() changes the default values of chunk options in a document.

Unnumbered sections

Add {-} at the end of the section title.

# Question 1: Variance and Covariance properties {-}
<!-- equivalently, you can use {.unnumbered} --> 
# Question 1: Variance and Covariance properties {.unnumbered}

Note that the section won’t be numbered but will show in the TOC.

If you want to further exclude it from the TOC:

# Question 1: Variance and Covariance properties {.unlisted .unnumbered}

Headings with # will appear in the file outline, which is a convenient feature. So use this method whenever possible.

One exception is level 2 headings in Bookdown:

By default Bookdown starts a new page for each level 2 heading. If you want to keep the style wihtout starting a new page, use an html tag. The heading won’t be numbered or included in TOC. However, a downside is that the heading won’t show up in the file outline either, making them harder to locate.
```
<h2>YAML metadata</h2>
```

Knitting in the global environment

rmarkdown::render("/Users/menghan/Library/CloudStorage/OneDrive-Norduniversitet/EK369E/Seminars/w1.rmd", envir=.GlobalEnv)

Advantages: fast; load and output results in the global environment; easy to inspect afterwards.

Rmd built-in themes for html output: https://rstudio4edu.github.io/rstudio4edu-book/rmd-themes.html

.Rmd documents can be edited in either source or visual mode. To switch into visual mode for a given document, use the Source or Visual button at the top-left of the document toolbar (or alternatively the Cmd+Shift+F4 keyboard shortcut).

Visual mode

Visual mode allows you to preview the effect after having compiled the markdown file.

❗️But it modifies your code silently, be cautions with visual mode.
More user-friendly in terms of providing drop down menus for editing.
Visual mode supports both traditional keyboard shortcuts (e.g. Cmd + B for bold) as well as markdown shortcuts (using markdown syntax directly). For example, enclose **bold** text in asterisks or type ## and press space to create a second level heading.
One bug for Visual mode is that inside bullet points, $ is automatically escaped as \$. In this case, use cmd+/ and choose inline math to insert an eqn.
When type inline equations, first type $ then the equation, then $ at last. Do not type $$ at one time. Otherwise, they will be escaped as regular text.

Comments in Rmd

In both html and pdf outputs, use the following to write true comments you don’t want to show in the rendered file.
```
 
```

Link to an external javascript

<SCRIPT language="JavaScript" SRC="my_jxscript.js"></SCRIPT>

Tips:

In general, you’d better leave at least one empty line between adjacent but different elements, e.g., a header and a paragraph. This is to avoid ambiguity to the Markdown renderer.

For example, the - in the list below cannot be recognized as a bullet point. You need to add a black line before the bullet list.
```
The result of 5
- 3 is 2.
```
Different flavors of Markdown may produce different results if there are no blank lines. 🙈🙈