R Markdown basic

A simple but sharp writing tool

Dr. Peng Zhao (✉ peng.zhao@xjtlu.edu.cn)

Department of Health and Environmental Sciences
Xi’an Jiaotong-Liverpool University

1 Learning objectives

• What is (R) Markdown.
• Basic rules of writing R Markdown documents.
• Generate html, docx, and pdf documents with R Markdown.
• Use markdown on online forums.

2 Markdown

2.1 Taking notes

2.2 What is Markdown

Markdown is a lightweight markup language for creating formatted text using a plain-text editor. John Gruber and Aaron Swartz created Markdown in 2004 as a markup language that is appealing to human readers in its source code form. Markdown is widely used in blogging, instant messaging, online forums, collaborative software, documentation pages, and readme files.

— Wikipedia

Briefly speaking, Markdown is a set of writing rules.

2.3 Basic Syntax

See Table 1.

You type	You get
# Chapter 1	headings
1. list...	numbered list
- list...	unnumbered list
*italic*	italic
**bold**	bold
PM~2.5~	subscript \(\text{PM}_{2.5}\)
R^2^	superscript \(\text{R}^2\)
$E = mc^2$	equations: \(E = mc^2\), \(G = \sqrt[n]{\prod_{i = 1}^{n} x_i}\)
[link](http://xjtlu.edu.cn)	hyperlink link
	insert an image
syntax for a table	insert a table

Table 1: Basic syntax of Markdown

2.4 Markdown Editors

• Plain text editor (e.g. Notepad in MS Windows)
• Notepad++ for MS Windows
• StackEdit.io
• Mark Text
• RStudio
• Typora

Demo:

• Write a Markdown document with a plain text editor
• Write a Markdown document with StackEdit.io. Export it into .html, .pdf, and .docx
• Write a Markdown document with RStudio. Knit it into .html, .pdf, and .docx

2.5 Application

• GitHub
• StackOverflow
• Capital of Statistics (in Chinese)
• ChatGPT

2.6 Maths expressions

• Obtain maths expressions from academic journals
  • Atmospheric Environment
  • Chinese Journal of Eco-Agriculture
• Obtain maths expressions from personal collections
  • ENV221 presentation documents.
  • My collections
• Write maths expressions by yourself
  • Search “latex equation editor online”
  • Learn basic rules

Demo: Insert an equation into your Markdown document.

3 R Markdown

R Markdown = R language + Markdown

3.1 .Rmd document

• Create
  • RStudio - File - New File - R Markdown - Document
• Save
• Open .Rmd with a plain text editor
• Export (knit) into .html, .docx, .pdf

For .pdf, install Tiny\(\TeX\) and tinytex:

install.packages('tinytex')
tinytex::install_tinytex()

3.2 Insert R chunks

• Hotkey: ctrl + alt + i

4 Further readings

• R Markdown Tutorial Lesson 1 – 9

5 Exercises

1. Convert this document into Markdown.
2. Create an R Markdown document, including the tasks and answers for Quiz 03 of ENV221.
3. Convert your slides for the oral presentation of ENV221 into R Markdown slides.
4. Leave a message on GitHub, using Markdown syntax.