Section 16 More on R Markdown
16.1 Tables
There are several options for producing tables in R Markdown.
16.1.1 Using Markdown
Here’s an example of making a table with the Markdown syntax. Note the use of : for specifying text alignment.
| column 1 | column 2 | column 3 |
|:----------|:---------:|----------:|
| this text | this text | this text |
| is left | is centre | is right |
| aligned | aligned | aligned |This is rendered as follows.
| column 1 | column 2 | column 3 |
|---|---|---|
| this text | this text | this text |
| is left | is centre | is right |
| aligned | aligned | aligned |
Online tools are available for generating Markdown syntax, for example https://www.tablesgenerator.com/markdown_tables.
16.1.2 Using knitr::kable()
The knitr package (Xie 2020), (Xie 2014), (Xie 2015) has the kable() function which can produce a table from a data frame. Here’s an example.
which is rendered (in html) as follows:
| mpg | cyl | disp | hp | drat | wt | qsec | vs | am | gear | carb | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Mazda RX4 | 21.0 | 6 | 160 | 110 | 3.90 | 2.620 | 16.46 | 0 | 1 | 4 | 4 |
| Mazda RX4 Wag | 21.0 | 6 | 160 | 110 | 3.90 | 2.875 | 17.02 | 0 | 1 | 4 | 4 |
| Datsun 710 | 22.8 | 4 | 108 | 93 | 3.85 | 2.320 | 18.61 | 1 | 1 | 4 | 1 |
| Hornet 4 Drive | 21.4 | 6 | 258 | 110 | 3.08 | 3.215 | 19.44 | 1 | 0 | 3 | 1 |
| Hornet Sportabout | 18.7 | 8 | 360 | 175 | 3.15 | 3.440 | 17.02 | 0 | 0 | 3 | 2 |
| Valiant | 18.1 | 6 | 225 | 105 | 2.76 | 3.460 | 20.22 | 1 | 0 | 3 | 1 |
16.2 Caching results for slow-running code
If some of your code takes a long time to run, it is preferable not to re-run it every time you edit your R Markdown document and want to re-compile it. It you use the code chunk option cache = TRUE, R will store (‘cache’) the results, and will only re-run the code chunk if it detects that something has changed.
Be careful if you use caching. For example, if you import a file and cache the results, R will not detect if the file contents change. When you knit your final version of your document, switch off all caching.
16.3 R Markdown for LaTeX users
The Markdown language is broadly the same as LaTeX for typesetting equations/maths notation, and so you can use LaTeX as normal for typesetting maths.
You can use any other LaTeX commands throughout your document. When producing pdf output, R Markdown will actually generate an intermediate .tex file, which is then compiled to pdf. However, these commands will be ignored if you knit to html or other formats.
Similarly, you can include html commands in your document; these will only work if you knit to html.
Try to keep to Markdown commands as far as possible. This will give you the most flexibility regarding your choice of output format (and you may wish to switch your output format in the future.)
For example, putting this in your document:
\section{Introduction}will only produce the desired section heading if you knit to pdf, but using this:
# Introductionwill give the desired section heading for any output format you produce.
16.4 The YAML header
The first part of an R Markdown document, the ‘header’ is used to specify information such as author and title, and can include extra commands to change the appearance of the document. These are commands are specified using another language called YAML. Here’s an example of a YAML header, with a few extra commands specified that you might find helpful.
---
title: "My Report Title"
author: "Jeremy Oakley"
date: "2024-01-27"
output:
pdf_document:
number_sections: true
html_document:
number_sections: true
fontsize: 11pt
urlcolor: blue
header-includes:
- \usepackage{bm}
---Indenting of particular lines does matter in YAML. Keep this is mind when copying YAML examples.
The command Sys.Date() is an R command which will insert today’s date (year-month-day format). The commands fontsize and urlcolor affect pdf output only. The final command
header-includes:
- \usepackage{bm}can be used to add commands (e.g. \usepackage{bm}) to the preamble in the LaTeX document for pdf output.