Basic Formatation

a. Manual line Break

To add a line break, you can type two or more spaces in the end of the line or use the break tag (<br>).

b.Headers type

# Header 1 ## Header 2 ### Header 3

c.Text Emphasis

- Italic Format
- Bold Format
- Subscript₁
- Superscript¹

*Italic* or _italic_
**Bold** or __Bold__
Subscript~1~
Superscript^1^

Lists

a. Ordered list

1. First Element
2. Second Element
      + Nested Element
      + Another Nested Element

b. Unordered list

* Text 
* Another text
      + Nested text
- Other option for list
      + Again nested text

Page Break

To add a page break, as the example above, you can simply type four or more dashes or stars:

------ or 
******

Blockquotes

a. Plain Code Block

Since the beginning of this session I am using this option to show how to apply each formatting introduced up to now. Using this it is possible to write some code in a fixed-width box without evaluating it:

      ```
      This text is displayed as it is **typed!** 
      ```

b. Blockquotes

Can be used to add some quotes in your markdown file, as in the following example.

“No medicine cures what happiness cannot”

Gabriel Garcia Marques
:)

> No medicine cures what happiness cannot  
> *Gabriel Garcia Marques*  
> :)

Usage examples:

Following you can find some usage examples of the mentioned options:

      html_document:
            code_folding: show
            toc: yes
            toc_depth: 1
            toc_float: yes
            code_download: yes
            highlight: haddock
            theme: lumen

Including section number:

output: 
      html_document:
            code_folding: show
            toc: yes
            toc_depth: 2
            toc_float: yes
            code_download: yes
            number_sections: true
            highlight: haddock
            theme: lumen

There are many themes available in Rmarkdown package, my preferred ones are: Flatly, Journal and Lumen.

Flatly theme:

Journal theme:

Lumen theme:

Echo Options

To insert some codes in the markdown document, the called code chunk, it is necessary to add three backticks like followed by {r}, where r indicates the language. To close the code chunk, add another three backticks in the end. Other option is using the shortcut Ctrl + Alt + i or if you are using R-Studio simply go to insert -> R and the chunk code will be added for you.

summary(cars)
##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00

It is possible to control the code output adding some chunk options inside the curly braces: {r }. Following, you can find some useful options that I use very frequently:

• eval: TRUE to evaluate the code chunk
  
• echo: TRUE to show the code in the output document
  
• results: If “hide” the text output will be hidden, “asis” for write a text as is.
  
• collapse: TRUE to merge output text and the code into a single code block in the output.
  
• Warning, message and error: Whether to show warnings, messages and error in the output document
• include: When include = FALSE, the whole code chunk is excluded in the output, but note that it will still be evaluated if eval = TRUE.
  
• cache: If caching is enabled, the same code chunk will not be evaluated the next time the document is compiled (if the code chunk was not modified), which can save you time.
  
• fig.width and fig.height: The (graphical device) size of R plots in inches. Ex: fig.width = 6 and fig.height = 4 or fig.dim = c(6, 4).
  
• out.width and out.height: The output size of R plots in the output document. These options may scale images. You can use percentages, e.g., out.width = ‘80%’ means 80% of the page width.
  
• fig.align: The alignment of plots. It can be ‘left’, ‘center’, or ‘right’.
  
• fig.cap: To include some figure caption.

For a better understanding of how those options works, let’s take a look into some practical examples as follow:

1. {r, include = FALSE}
   • Code not shown
     
   • results not shown
2. {r, echo = FALSE}
   • Code not shown
   • results shown

##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00

3. {r, results = ‘hide’}
   • Code shown
     
   • Results not shown

summary(cars)

4. {r, collapse=TRUE}
   • To merge the code and the output

summary(cars)
##      speed           dist       
##  Min.   : 4.0   Min.   :  2.00  
##  1st Qu.:12.0   1st Qu.: 26.00  
##  Median :15.0   Median : 36.00  
##  Mean   :15.4   Mean   : 42.98  
##  3rd Qu.:19.0   3rd Qu.: 56.00  
##  Max.   :25.0   Max.   :120.00

5. {r, out.width=‘30%’, fig.align=‘center’, fig.cap=‘Amazing Hong Kong’}
   • Another option for including images and captions.

knitr::include_graphics('img/timon-studler-49992-unsplash.jpg')

Figure 1: Amazing Hong Kong

6. {r, fig.align=‘center’, fig.width = 6, fig.height=4}
   • It is possible to adjust the graph size as well its alignment in the output document

ggplot(cars, aes(x=speed, y=dist)) +
      geom_point(alpha=1) + 
      labs(title = "Speed vs. Distance", x = "Speed", y = "Distance") + 
      theme_bw()

There are many options available for control the Code Chunk output, if you want more information about it, the following links are very good references:
https://yihui.name/knitr/options/
https://bookdown.org/yihui/rmarkdown/r-code.html
https://www.overleaf.com/learn/latex/Positioning_images_and_tables

Inline Code

If you wants to add just a small code expression in the markdown text, just add one backticks before and another one after the code expression.

For example:
- The total speed in Cars dataset is 770
- The total distance in Cars dataset is 2149

Inline and display mode

If you are typing just a small formula, you might just want to add it in the line that you are typing. for example: “This is an inline example formula: \(E=mc^2\)”

      "This is an inline example formula: $E=mc^2$"

But, if you are typing a very long expression, you might think that is better to use the display mode:
$$a^n + b^n = (a - b)(a^{n-1} + a^{n-2}b + a^{n-3}b^2 + ... + ab^{n-2} + b^{n-1})$$

   $$a^n + b^n = (a - b)(a^{n-1} + a^{n-2}b + a^{n-3}b^2 + ... + ab^{n-2} + b^{n-1})$$

Symbols:

Some useful symbol formatations:

Greek Letters

Index

\[ \begin{align} x_i, x_{i} && \text{(Subscript)}\\ x^2 && \text{(Superscript)}\\ x^2_i,~x^2_{i,j} && \text{(Combined)}\ \end{align} \]

x_i, x_{i} (Subscript)
x^2 (Superscript)
x^2_i, x^2_{i,j} (Combined)  

Expressions

$\sqrt{x}$

$x=\frac{1}{1+e^{\beta_0+\beta_{1}\times y}}$   

$x=\left(\frac{1}{1+e^{\beta_0+\beta_{1}\times y}}\right)$

$\sum_{i=1}^n(y_i-\hat{y})^2$

$$\int_0^{a} x^k~dx$$

$$ \frac{\partial u}{\partial t}
   = h^2 \left( \frac{\partial^2 u}{\partial x^2}
      + \frac{\partial^2 u}{\partial y^2}
      + \frac{\partial^2 u}{\partial z^2} \right) $$

$$\lim_{x \to +\infty} \frac{3x^2 +7x^3}{x^2 +5x^4} = 3$$

Matrices

\[\mathbf{X} = \left[\begin{array} {rrr} 2 & 4 & 6 \\ 8 & 10 & 12 \\ 14 & 16 & 18 \end{array}\right]\]

$$\mathbf{X} = \left[\begin{array}
{rrr}
2 & 4 & 6 \\
8 & 10 & 12 \\
14 & 16 & 18
\end{array}\right]$$

For operations with matrix you can also use \(\mathbf{y}=\mathbf{X}\beta\), for example.

$\mathbf{y}=\mathbf{X}\beta$

Alignment and comments:

You can use “~” to add some spaces in the formula: \[ x_{i} + y_{i} \ge 0 ~~~~~~~\forall~i \in \mathbb{R} \]

$$ x_{i} + y_{i} \ge 0 ~~~~~~~\forall~i \in \mathbb{R} $$

The formula inserted in “index” topic, wasn’t completely shown at that time. To write formulas together with comments, is necessary to use the following syntax:

$$
\begin{align}
x_i, x_{i} && \text{(Subscript)}\\
x^2 && \text{(Superscript)}\\
x^2_i,~x^2_{i,j} && \text{(Combined)}\  
\end{align}
$$

Besides that, when solving large expressions, might be useful to use some alignment:

\[\begin{align} 5\times a~+~10 &=30 \\ 5\times a &= 20 \\ a &= 4 \end{align}\]

$$\begin
      5\times a~+~10 &=30 \\
      5\times a &= 20 \\
      a &= 4
\end$$