Markdown is a textual format proposed by John Gruber that can be easily converted into several different formats

Markdown is intended to be as easy-to-read and easy-to-write as is feasible.

• should be publishable as-is, as plain text, without looking like it’s been marked up with tags or formatting instructions
• syntax is comprised entirely of punctuation characters, carefully chosen so as to look like what they mean.
  • E.g., asterisks around a word actually look like *emphasis*.

Several tools are able to convert markdown to HTML.

The most complete tool is Pandoc

• able to convert to and from several formats https://pandoc.org
• used within R Studio to perform conversions

In R Studio you can

• click on

• use the function: render(), e.g.:

  rmarkdown::render('foo.Rmd', 'html_document')

• Emphasis: *Emphasis*
• Bold: **Bold**
• Superscript 2³¹ : 2^31^
• Subscript x_i : x~i~
• PoliTo : [PoliTo](https://www.polito.it)
• : ![](Knit.png)

• Paragraph are text blocks separate by empty lines

• Headings

  # Level 1 heading
  ## Level 2 heading
  ### Level 3 heading

  alternate syntax

  Level 1 heading
  ===============
  
  Level 2 heading
  ---------------

Fenced code blocks

• delimited by three (or more) backticks ```

```
Verbatim text
```

• Quotation with > in first column

Making the simple complicated is commonplace; making the complicated simple, awesomely simple, that’s creativity

— Charles Mingus

• Bullet lists start with *, -, or +
• Numbered lists start with a number
• Can be nested with indentation

- Top item
    1. 2nd level
    2. another

• Top item
  1. 2nd level
  2. another

Tables are built by

• header: column labels separated by |
• rule: sequence of dashes - separated by | at column breaks
  • initial : means align left
  • final : means align right
  • both means align center
• rows: content cells, separated by |

ID   | Name    | Points  |
:----|:-------:|--------:|
 123 | aleph   |  987    |
 666 | bet     |  1234   |
 456 | gimel   |  98     |

• Inline maths within $
• Equations within $$
• Uses LaTeX math , e.g.,

• Code blocks starting with ```{r ... }
  • r stands for R language (can be e.g. python, java)
  • followed by an optional label for the chunk
  • followed by additional chunk parameters
    • include whether to include chunk results in output
    • echo whether to report source in output
    • eval whether to evaluate at all the code chunk
• By default code is echoed and output is added to result

Result of expressions can be placed inline within regular markdown enclosed between `r and `.

- A sum of squares: `r 3^2+5^2`.

Is rendered as:

• A sum of squares: 34.

Plots produced by the code are addet in the resulting document.

Userful parameters are fig.width, fig.height to define the dimension of the reulting plot, it can control:

• aspect ratio: w/h
• resolution: larger values imply higher resolution and smaller elements (e.g. chars)

x = cos(1:100/50*pi); y = sin(1:100/25*pi)
plot(x,y)

Parameters: fig.width=9,fig.height=3

x = cos(1:100/50*pi); y = sin(1:100/25*pi)
plot(x,y)

It is possible to format the content of a data frame as a table using the knitr::kable() function

knitr::kable(courses)

The alternative is a text-based rendering like in the console.

courses

##    code           course semester credits
## 1 15AHM        Chemistry        1       8
## 2 12BHD Computer science        1       8
## 3 16ACF       Calculus I        1      10
## 4 01PNN     Free Credits        2       6
## 5 01RKC   Linear Algebra        2      10
## 6 17AXO        Physics I        2      10

R markdown document can include a header block that contains meta-data.

• is included between lines with ---
• uses the YAML syntax.

---
title: Habits
author: John Doe
date: March 22, 2048
output: html_document
---

The output parameter can be:

• R Notebook: html_notebook
• HTML document: html_document
• PDF document: pdf_document
  • Requires LaTeX installation, e.g. package tinytex
• Word document word_document
• ODT document odt_document
• …

A notebook is a R markdown document

• chunks that can be executed independently and interactively,
• output of execution appears immediately beneath the input.

A preview can be enabled

• it shows the HTML rendering of the document
  • only evaluated chunks are included
• it is updated on save

Basic chunk behavior active in any Rmd document

• execute current chunk
  • Ctrl + Shift + Enter / Cmd + Shift + Enter
  • green arrow on top right of chunk
• execute current statement
  • Ctrl + Enter / Cmd + Enter
• insert new chunk
  • Ctrl + Alt + I / Cmd + Option + I
  • Insert button on top of editor pane

When saved a notebook creates a .nb.html file

• the file contains the output of the evaluated chunks
• it can be viewed with a browser
• it contains also the source R markdown
• when opened in RStudio, source is extracted in placed in a .Rmd file.

library(leaflet)
leaflet() %>% addTiles() %>%
  setView(7.659, 45.063, zoom = 16)

• R
  • Download at: https://cran.r-project.org
• R-Studio Desktop
  • Download at: https://rstudio.com/products/rstudio/

• John Gruber. “Markdown: Syntax”, 2004
  • https://daringfireball.net/projects/markdown/syntax
• John MacFarlane. “Pandoc’s User guide”, 2020.
  • https://pandoc.org/MANUAL.html
• RYihui Xie, J. J. Allaire, Garrett Grolemund. “R Markdown: The Definitive Guide”, Chapman & Hall/CRC, 2020.
  • https://bookdown.org/yihui/rmarkdown/
• Vv.Aa. “Overleaf help - Mathematical expressions”
  • https://www.overleaf.com/learn/latex/Mathematical_expressions