Introduction to R Markdown

1. Headings

Headings are proceed by #. The number of # at the beginning of a line indicates the level of heading (main section, sub section, sub-sub section, etc.)

Here is an illustration.

H1 level

This is header level 1

H2 level

This is header level 2

H3 level

This is header level 3 and so on.

2. Text Formatting

This text is in italics. And so is this text.

This text is in bold. And so is this text.

This text is rendered with strikethrough.

3. Bullet Points

• Item 1

• Item 2

  • 2a
  • 2b

or

• Item
• Another item

or

• Item
• Another item

4. Numbered List

1. Item one
2. Item two
3. Item three

5. Code Chunks

Example 1

set.seed(20205)
x <- rnorm(10)
summary(x)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
## -2.1341 -1.1879  0.4502 -0.1464  0.7082  1.0402

Example 2: Remove hashtag in the output

set.seed(20205)
x <- rnorm(10)
summary(x)

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
-2.1341 -1.1879  0.4502 -0.1464  0.7082  1.0402 

Example 3: Display only the output

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
-2.1341 -1.1879  0.4502 -0.1464  0.7082  1.0402 

Example 4: Display only the code

set.seed(20205)
x <- rnorm(10)
summary(x)

Example 5: Code chunk with figures

library(tidyverse)

## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
## ✔ ggplot2 3.3.6.9000     ✔ purrr   0.3.4     
## ✔ tibble  3.1.8          ✔ dplyr   1.0.9     
## ✔ tidyr   1.2.0          ✔ stringr 1.4.1     
## ✔ readr   2.1.2          ✔ forcats 0.5.2     
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()

qplot(data=iris, x=Sepal.Length, y=Sepal.Width, geom="point")

## Warning: `qplot()` was deprecated in ggplot2 3.4.0.

Example 6: Hide warnings and messages

library(tidyverse)
qplot(data=iris, x=Sepal.Length, y=Sepal.Width, geom="point")

Example 7: Include a figure caption

qplot(data=iris, x=Sepal.Length, y=Sepal.Width, geom="point")

Scatterplot of Sepal Width vs Sepal Length

Example 8: Control figure size

qplot(data=iris, x=Sepal.Length, y=Sepal.Width, geom="point")

Scatterplot of Sepal Width vs Sepal Length

6. Mathematical Formulae

The general formula for the probability density function of the normal distribution with mean \(\mu\) and variance \(\sigma\) is given by

\[ f_X(x) = \frac{1}{\sigma\sqrt{(2\pi)}} e^{-(x-\mu)^2/2\sigma^2}. \]

More examples

Example 1: Fraction ()

\[\frac{a}{b}=\frac{c}{b}\]

Example 2: Bold math symbols

\[\mathbf{(X'X)^{-1}X'Y}\]

Example 3: Summation, Superscript (^) and Subscript (_)

\[\sum_{i=1}^{n}{x_i^2}\]

Example 4: Equation with multiple lines

Example 4.1:

\[ \begin{eqnarray} P(|X-\mu| > k) & = & P(|X-\mu|^2 > k^2)\\ & \leq & \frac{\mathbb{E}\left[|X-\mu|^2\right]}{k^2}\\ & \leq & \frac{\mathrm{Var}[X]}{k^2} \end{eqnarray} \]

Example 4.2:

\[ \begin{eqnarray} X & \sim & \mathrm{N}(0,1)\\ Y & \sim & \chi^2_{n-p}\\ R & \equiv & X/Y \sim t_{n-p} \end{eqnarray} \]

Example 5: Parenthesis ((…))

\[\left(\sum_{i=1}^{n}{i}\right)^2\]

7. Tables

Method 1

library(knitr)
kable(iris[1:5,], caption="A knitr kable 1")

A knitr kable 1

Sepal.Length	Sepal.Width	Petal.Length	Petal.Width	Species
5.1	3.5	1.4	0.2	setosa
4.9	3.0	1.4	0.2	setosa
4.7	3.2	1.3	0.2	setosa
4.6	3.1	1.5	0.2	setosa
5.0	3.6	1.4	0.2	setosa

kable(summary(iris), caption="A knitr kable 2")

A knitr kable 2

	Sepal.Length	Sepal.Width	Petal.Length	Petal.Width	Species
	Min. :4.300	Min. :2.000	Min. :1.000	Min. :0.100	setosa :50
	1st Qu.:5.100	1st Qu.:2.800	1st Qu.:1.600	1st Qu.:0.300	versicolor:50
	Median :5.800	Median :3.000	Median :4.350	Median :1.300	virginica :50
	Mean :5.843	Mean :3.057	Mean :3.758	Mean :1.199	NA
	3rd Qu.:6.400	3rd Qu.:3.300	3rd Qu.:5.100	3rd Qu.:1.800	NA
	Max. :7.900	Max. :4.400	Max. :6.900	Max. :2.500	NA

Method 2

Colons can be used to align columns.

Column 1	Column 2	Column 3
Tim	Positive	USA
Jane	Negative	UK
Cathy	Negative	AUS

There must be at least 3 dashes separating each header cell. The outer pipes (|) are optional, and you don’t need to make the raw Markdown line up prettily. You can also use inline Markdown.

Index No	Assignment 1	Assignment 2
ASXXX	apply	Factors
1	2	3

8. Include an External Image