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EDAV Fall 2021 Mon/Wed Community Contributions

19 Common R markdown syntax cheatsheet

Yufan Cao and Yingfei Zhu

R Markdown is a file format for making dynamic documents with R. It provides an authoring frame work of data science. The R Markdown has two main purpose: 1. Save and execute code 2. Generate high quality reports that can be shared with audience

R Markdown documents can support various of dynamic and static output format, such as pdf or Html. The syntax of R Markdown is also important, students need to learn how to write Markdown syntax to produce a concise and clear reports.

19.1 Markdown Syntax

19.1.1 Workflow

    1. Open a new.Rmd file in the RStudio IED by goting to File > New File > R Markdown
    1. Embed code in chunks, run code by line, by chunk, or all at once.
    1. Write text and add tables, images, figures, and citations. Format with Markdown syntax of the RStudio Visual Markdown Editor.
    1. Set Output format(s) and options in the YAML header. Customize themes or add parameters to execute or add interactivity with Shiny.
    1. Save and render the whole document. Knit periodically to preview your work as you write.
    1. Present or share your work.

19.1.2 Inline Formatting

    1. Italic inline text: surrounded by underscores or asterisks (e.g., _text_ or *text*)
    1. Bold text: produced using a pair of double asterisks or surrounded by two underscores (e.g., **text** or `__text_``).
    1. Turn text to a subscript: using a pair of tildes (~) (e.g., H~3~PO~4~ renders H3PO4)
    1. Turn text to a superscript: using a pair of carets(^) (e.g., Cu^2+^ renders Cu2+)
    1. add line in the text: using two pair of tildes(~~), (e.g., ~~text~~ renders text)
    1. hyperlink: use the syntax [text](link), (e.g.,link` renders link)
    1. Mark text as inline code: use a pair of backticks, (e.g., `code`), to include n literal backticks, use at least n+1 backticks outside, (e.g., you can use three backticks to preserve two backtick inside: ``` ``code`` ```, which is rendered as ``code`` )

```

text

``` will renders

text
    1. >block quotes will render as

block quotes

    1. Equation: $e^{i \pi} +1 = 0$ renders \(e^{i \pi} +1 = 0\)
    1. Equation blocks: $$E = mc^{2}$$ renders \[E = mc^{2}\]
    1. ‘- ordered list’ renders

  • ordered list

    1. text size: use number sign # to adjust the text size for header, as the # increase, the size of header decrease.

(e.g., # Header renders

19.3 Mathematical Expression

19.3.1 Mathematical notation

In side a text chunk of rmd file, you can use mathematical notation with dollar sign in two different styles.

Inline LaTeX equations can be written if you surround it by a pair of dollar signs using the LaTeX syntax. Example: $f(k) = {n \choose k} p^{k} (1-p)^{n-k}$ will produce \(f(k) = {n \choose k} p^{k} (1-p)^{n-k}\)

Display style math expressions can be written in a pair of double dollar signs. Example $$f(k) = {n \choose k} p^{k} (1-p)^{n-k}$$ will produce \[f(k) = {n \choose k} p^{k} (1-p)^{n-k}\]

Notice: there is no space between the $ and your mathematical notation. You can also use math environments inside $ $ or $$ $$

19.3.2 Common Mathematical Symbol

Math Mode Accents

Output Syntax
\(x^{n}\) $x^{n}$
\(x_{n}\) $x_{n}$
\(\overline{x}\) $\overline{x}$
\(\hat{x}\) $\hat{x}$
\(\tilde{x}\) $\tilde{x}$
\(\acute{x}\) $\acute{x}$
\(\tilde{x}\) $\vec{x}$
\(\dot{x}\) $\dot{x}$

Binary Relation

Output Syntax
\(x = y\) $x = y$
\(x < y\) $x < y$
\(x > y\) $x > y$
\(x \approx y\) $x \approx y$
\(x \ne y\) $x \ne y$or$x \neq y$
\(x \le y\) $x \le y$
\(x \ge y\) $x \ge y$
\(x \equiv y\) $x \equiv y$
\(x \ll y\) $x \ll y$
\(x \gg y\) $x \gg y$
\(x \doteq y\) $x \doteq y$
\(x \prec y\) $x \prec y$
\(x \succ y\) $x \succ y$
\(x \sim y\) $x \sim y$
\(x \preceq y\) $x \preceq y$
\(x \succeq y\) $x \succeq y$
\(x \simeq y\) $x \simeq y$
\(x \subset y\) $x \subset y$
\(x \in A\) $x \in A$
\(x \notin A\) $x \notin A$
\(A \ni x\) $x \ni A$or$A \owns x$
\(x \subset B\) $x \subset B$
\(x \subseteq B\) $x \subseteq B$
\(A \cup B\) $A \cup B$
\(A \cap B\) $A \cap B$
\(A \perp B\) $A \perp B$
\(A \bowtie B\) $A \bowtie B$
\(A \propto B\) $A \propto B$
\(A \mid B\) $A \mid B$
\(A \parallel B\) $A \parallel B$

Operators / Statistical Expression

Output Syntax
\(\frac{a}{b}\) $\frac{a}{b}$
\(\frac{\partial f}{\partial x}\) $\frac{\partial f}{\partial x}$
\(\binom{n}{k}\) $\binom{n}{k}$
\(x_{1} + x_{2} + \cdots + x_{n}\) $x_{1} + x_{2} + \cdots + x_{n}$
\(x_{1}, x_{2}, \dots, x_{n}\) $x_{1}, x_{2}, \dots, x_{n}$
\(\mathbf{x} = \langle x_{1}, x_{2}, \dots, x_{n}\rangle\) $\mathbf{x} = \langle x_{1}, x_{2}, \dots, x_{n}\rangle$
\(|A|\) $|A|$
\(X \sim {\sf Binom}(n, \pi)\) $X \sim {\sf Binom}(n, \pi)$ (sf for “slide font”)
\(\mathrm{P}(X \le x) = {\tt pbinom}(x, n, \pi)\) $\mathrm{P}(X \le x) = {\tt pbinom}(x, n, \pi)$ (tt for “typewriter type”)
\(P(A \mid B)\) $P(A \mid B)$
\(\mathrm{P}(A \mid B)\) $\mathrm{P}(A \mid B)$ (mathrm for “math roman font”
\(\{1, 2, 3\}\) $\{1, 2, 3\}$
\(\sin(x)\) $\sin(x)$
\(\log(x)\) $\log(x)$
\(\int_{a}^{b}\) $\int_{a}^{b}$
\(\left(\int_{a}^{b} f(x) \; dx\right)\) $\left(\int_{a}^{b} f(x) \; dx\right)$
\(\left[\int_{-\infty}^{\infty} f(x) \; dx\right]\) $\left[\int_{-\infty}^{\infty} f(x) \; dx\right]$
\(\left. F(x) \right|_{a}^{b}\) $\left. F(x) \right|_{a}^{b}$
\(\sum_{x = a}^{b} f(x)\) $\sum_{x = a}^{b} f(x)$
\(\prod_{x = a}^{b} f(x)\) $\prod_{x = a}^{b} f(x)$
\(\lim_{x \to \infty} f(x)\) $\lim_{x \to \infty} f(x)$
\(\displaystyle \lim_{x \to \infty} f(x)\) $\displaystyle \lim_{x \to \infty} f(x)$

Other symbols

Output Syntax
\(\because\) $\because$
\(\therefore\) $\therefore$
\(\forall\) $\forall$
\(\exists\) $\exists$
\(\partial\) $\partial$
\(\emptyset\) $\emptyset$
\(\nabla\) $\nabla$
\(\triangle\) $\triangle$
\(\angle\) $\angle$
\(\surd\) $\surd$
\(\S\) $\S$
\(\varpropto\) $\varpropto$
\(\diamondsuit\) $\diamondsuit$
\(\heartsuit\) $\heartsuit$
\(\clubsuit\) $\clubsuit$
\(\spadesuit\) $\spadesuit$

19.3.3 Matrix

  • Matrix with no bracket
$$X = \begin{array}{ccc}
x_{11} & x_{12} & x_{13}\\
x_{21} & x_{22} & x_{23}
\end{array}$$

\[X = \begin{array}{ccc} x_{11} & x_{12} & x_{13}\\ x_{21} & x_{22} & x_{23} \end{array}\]

  • With square bracket
$$X = \begin{bmatrix}
x_{11} & x_{12} & x_{13}\\
x_{21} & x_{22} & x_{23}
\end{bmatrix}$$

\[X = \begin{bmatrix} x_{11} & x_{12} & x_{13}\\ x_{21} & x_{22} & x_{23} \end{bmatrix}\]

  • With parentheses
$$X = \begin{pmatrix}
x_{11} & x_{12} & x_{13}\\
x_{21} & x_{22} & x_{23}
\end{pmatrix}$$

\[X = \begin{pmatrix} x_{11} & x_{12} & x_{13}\\ x_{21} & x_{22} & x_{23} \end{pmatrix}\]

  • With determinant / vertical bar bracket
$$\begin{vmatrix} 
   a_{11} & a_{12} & a_{13}  \\
   a_{21} & a_{22} & a_{23}  \\
   \end{vmatrix} $$

\[\begin{vmatrix} a_{11} & a_{12} & a_{13} \\ a_{21} & a_{22} & a_{23} \\ \end{vmatrix}\]

  • With curly brackets
$$\begin{Bmatrix} 
   a_{11} & a_{12} & a_{13}  \\
   a_{21} & a_{22} & a_{23}  \\
   \end{Bmatrix} $$

\[\begin{Bmatrix} a_{11} & a_{12} & a_{13} \\ a_{21} & a_{22} & a_{23} \\ \end{Bmatrix} \]

  • With double vertical bar brackets
$$\begin{Vmatrix} 
   a_{11} & a_{12} & a_{13}  \\
   a_{21} & a_{22} & a_{23}  \\
   \end{Vmatrix} $$

\[\begin{Vmatrix} a_{11} & a_{12} & a_{13} \\ a_{21} & a_{22} & a_{23} \\ \end{Vmatrix} \]

  • Small inline matrix

Small inline matrix$\big(\begin{smallmatrix} a & b\\ c & d \end{smallmatrix}\big)$ will produce
Small inline matrix\(\big(\begin{smallmatrix} a & b\\ c & d \end{smallmatrix}\big)\)

19.3.4 Greek letters

Output Syntax
\(\alpha A\) $\alpha A$
\(\beta B\) $\beta B$
\(\gamma \Gamma\) $\gamma \Gamma$
\(\delta \Delta\) $\delta \Delta$
\(\epsilon \varepsilon E\) $\epsilon \varepsilon E$
\(\zeta Z \sigma \,\!\) $\zeta Z \sigma \,\!$
\(\eta H\) $\eta H$
\(\theta \vartheta \Theta\) $\theta \vartheta \Theta$
\(\iota I\) $\iota I$
\(\kappa K\) $\kappa K$
\(\lambda \Lambda\) $\lambda \Lambda$
\(\mu M\) $\mu M$
\(\nu N\) $\nu N$
\(\xi\Xi\) $\xi\Xi$
\(o O\) $o O$
\(\pi \Pi\) $\pi \Pi$
\(\rho\varrho P\) $\rho\varrho P$
\(\sigma \Sigma\) $\sigma \Sigma$
\(\tau T\) $\tau T$
\(\upsilon \Upsilon\) $\upsilon \Upsilon$
\(\phi \varphi \Phi\) $\phi \varphi \Phi$
\(\chi X\) $\chi X$
\(\psi \Psi\) $\psi \Psi$
\(\omega \Omega\) $\omega \Omega$

19.3.5 Aligning Equations

If you want a sequence of aligned equations (often very useful for demonstrating algebraic manipulation or for plugging values into equations), use \begin{align*} ... \end{align*}. Separate lines with \\ and use & to mark where things should line up. Note: No dollar signs are needed for mathematical expression in this method.

Example:

$\begin{aligned}
AR(p): Y_i &= c + \epsilon_i + \phi_i Y_{i-1} \dots \\
Y_{i} &= c + \phi_i Y_{i-1} \dots
\end{aligned}$

\(\begin{aligned} AR(p): Y_i &= c + \epsilon_i + \phi_i Y_{i-1} \dots \\ Y_{i} &= c + \phi_i Y_{i-1} \dots \end{aligned}\)

19.4 Reference

Latex math symbols. Kapeli. (n.d.). Retrieved October 28, 2021, from
https://kapeli.com/cheat_sheets/LaTeX_Math_Symbols.docset/Contents/Resources/Documents/index.

Pruim, R. (2016, October 19). Mathematics in R markdown. Retrieved October 28, 2021, from
https://rpruim.github.io/s341/S19/from-class/MathinRmd.html.

R markdown : : Cheat sheet - ETH Z. (n.d.). Retrieved October 28, 2021, from
https://ethz.ch/content/dam/ethz/special-interest/math/statistics/sfs/Education/Advanced%20Studies%20in%20Applied%20Statistics/course-material-1719/Datenanalyse/rmarkdown-2.pdf.

Yihui Xie, C. D. (2021, October 7). R markdown cookbook. 5.2 Indent text. Retrieved October 28, 2021, from https://bookdown.org/yihui/rmarkdown-cookbook/indent-text.html.

Yihui Xie, J. J. A. (2021, April 9). R markdown: The definitive guide. Home. Retrieved October 28, 2021, from
https://bookdown.org/yihui/rmarkdown/.