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Fundamentals of Data Science for EESS





R session 02 - R markdown

Daniel Vaulot

2021-01-20

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Outline



  • What is Markown ?
  • Rmarkdown syntax
  • R chunks
  • Some applications
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What is markdown ?

  • Created in 2004 by John Gruber and Aaron Swartz

  • Goal : "to write using an easy-to-read and easy-to-write plain text format, optionally convert it to structurally valid HTML".

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What is markdown ?

  • Created in 2004 by John Gruber and Aaron Swartz

  • Goal : "to write using an easy-to-read and easy-to-write plain text format, optionally convert it to structurally valid HTML".

Many flavors...

  • MultiMarkdown
  • GitHub Flavored Markdown (GFM)
  • Pandoc
  • CommonMark
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Rmarkdown

Mix

  • Markdown

    • paragraph structure
    • comments
    • links

  • R code ("chunks")

  • Output of R code

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Your first Rmarkdown file

Who has not been able to install Rmarkdown and Latex ?

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Your first Rmarkdown file

Who has not been able to install Rmarkdown and Latex ?

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Your first Rmarkdown file

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Your first Rmarkdown file

Knit to HTML

Save to "xxx.Rmd"

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Your first Rmarkdown file

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Your first Rmarkdown file

Knit of pdf

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Your first Rmarkdown file

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Markdown syntax

Headings

# Heading - level 1   
## Heading - level 2
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Markdown syntax

Headings

# Heading - level 1   
## Heading - level 2

Heading - level 1

Heading - level 2

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Markdown syntax

Paragraphs

Paragraphs are separated
by a blank line.
Two spaces at the end of a line  
produces a line break.
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Markdown syntax

Paragraphs

Paragraphs are separated
by a blank line.
Two spaces at the end of a line  
produces a line break.

Paragraphs are separated by a blank line.

Two spaces at the end of a line
produces a line break.

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Markdown syntax

Formatting

_italic_, *italic*, **bold**, `monospace`.
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Markdown syntax

Formatting

_italic_, *italic*, **bold**, `monospace`.

italic, italic, bold, monospace.

Do not mix straight and backward quotes

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Markdown syntax

Bullet lists

Bullet list:
  * apples
  * oranges
  * pears
      * passe crassane (4 spaces to indent)
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Markdown syntax

Bullet lists

Bullet list:
  * apples
  * oranges
  * pears
      * passe crassane (4 spaces to indent)
  • apples
  • oranges
  • pears
    • passe crassane
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Markdown syntax

Numbered lists

Numbered list:
1. wash
1. rinse
1. repeat
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Markdown syntax

Numbered lists

Numbered list:
1. wash
1. rinse
1. repeat
  1. wash
  2. rinse
  3. repeat
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Markdown syntax

  [Text of the link](URL of the link)
# Example
  [Markdown syntax](https://www.markdownguide.org/basic-syntax/)
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Markdown syntax

  [Text of the link](URL of the link)
# Example
  [Markdown syntax](https://www.markdownguide.org/basic-syntax/)

Markdown syntax

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Markdown syntax

Images

  ![Image name](URL of the link - can also be a local file on your computer)
# Example
  ![](https://i.pinimg.com/originals/1c/b7/24/1cb724b545de717ed0430e9d46e78eea.jpg)
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Markdown syntax

Images

  ![Image name](URL of the link - can also be a local file on your computer)
# Example
  ![](https://i.pinimg.com/originals/1c/b7/24/1cb724b545de717ed0430e9d46e78eea.jpg)

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Markdown syntax

Tables

ID | First | Last
--- | --- | ---
1 | Jo | Biden
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Markdown syntax

Tables

ID | First | Last
--- | --- | ---
1 | Jo | Biden
ID First Last
1 Jo Biden
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Rmarkdown conversion

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Rmarkdown conversion

  • knitr : R library

  • Pandoc : command line tool

    • Converts from md to pdf, html, docx...
# HTML
> pandoc test1.md -f markdown -t html -s -o test1.html
# pdf
> pandoc test1.md -s -o test1.pdf

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The Rmarkdown file

File structure

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The Rmarkdown file

Knit process

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The Rmarkdown file

Output

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R Chunks

Insert R chunk

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R Chunks

Run R chunk

  • Two options

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R Chunks

Option 1: Run R chunk inside Rmd file

  • Use when building and debugging an Rmd file

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R Chunks

Option 2: Knit R chunk to HTML

  • Use for final production

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R Chunks

Options for R chunks

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R Chunks

Useful options


Options Default value Aim
echo TRUE Print code (= FALSE in a report for example)
eval TRUE Evaluate code (= FALSE if want to show code only)
warning TRUE Warning message (= FALSE to remove long warnings)
message TRUE Messages (= FALSE to remove long messages)
cache FALSE If TRUE only modified chunks will be evaluated
very useful for computing heavy codes
fig.height inches
fig.width inches
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R Chunks

Set defaults options

  • Insert in a R chunk at the beginning of your Rmarkdown file
  • Option CACHE = true reduce compiling time
  knitr::opts_chunk$set(fig.width=6, fig.height=6, 
                        eval=TRUE, 
                        cache=TRUE,
                        echo=TRUE,)
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What can you do with Rmarkdown ?

Document your data analyses

  • If the data changes, you can re-run analysis in a matter of minutes
  • More and more journal request analyses scripts
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What can you do with Rmarkdown ?

Presentation

https://github.com/yihui/xaringan

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What can you do with Rmarkdown ?

Posters

https://github.com/brentthorne/posterdown

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What can you do with Rmarkdown ?

Curriculum vitae

https://cloud.r-project.org/web/packages/vitae/index.html

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What can you do with Rmarkdown ?

Website

https://bookdown.org/yihui/blogdown/

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What did you learn ?




  • Rmarkdown: mix text, R chunk, R output
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What did you learn ?




  • Rmarkdown: mix text, R chunk, R output
  • Compile to HTML or to PDF
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What did you learn ?




  • Rmarkdown: mix text, R chunk, R output
  • Compile to HTML or to PDF
  • Can be used for many different purposes
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What did you learn ?




  • Rmarkdown: mix text, R chunk, R output
  • Compile to HTML or to PDF
  • Can be used for many different purposes
  • Use to document your analysis process (for papers...)
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Outline



  • What is Markown ?
  • Rmarkdown syntax
  • R chunks
  • Some applications
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