Markdown is a text-to-HTML conversion tool for web writers. Markdown allows you to write, using an easy-to-read, easy-to-write plain text format, and then convert it to structurally valid XHTML (or HTML).

--John Gruber, Creator of Markdown (http://daringfireball.net/projects/markdown/)

This simplification, and the fact that it is akin to the markup language, enables authors to perform a fast and intuitive formatting of text. Following are some examples:

• The use of hashes will create headlines:

  # This is an H1 heading
  
  ## This is an H2 heading
  
  ### This is an H3 heading
  
  #### This is an H4 heading

• If you want to create an ordered list, you can use numbers with a period:

  1. Blue
  
  2. Green
  
  3. Black
  
  4. Yellow

• For unordered lists, you can use * (asterisks), + (plusses), and – (hyphens) as interchangeable list markers, instead of numbers.

What is literate programming?

Literate programming refers to the writing of computer programs in such as a way that they are mainly readable for human beings. Technically, it means that both the documentation and the source code of a respective program are available in a single file. The following characteristics of a literate programming system are required:

• The source code and comments can be mixed.
• The source code sections can be arranged in any order. The literate programming system automatically composes the code as machine-readable and in an executable sequence.
• The literate programming system automatically creates a human-readable document with a table of contents, references, citation, and other similar parts.

The process of creating human-readable documents is called weaving, while the creation of machine-readable documents is called tangling.

To use the principles of literate programming with R and RStudio, you can either use Sweave or the knitr package.

A brief side note on Sweave

Sweave is part of every R installation and was created by Prof. Friedrich Leisch. It uses LaTeX as documentation and R as the programming language. A heavy usage of Sweave is limited by the fact that LaTeX is a comparatively complex markup language. Furthermore, this tool lacks modern and important features such as the caching and using of various programming languages at once.

If you want to create an R Sweave document in RStudio, click on the new file button and choose R Sweave:

For more information about Sweave please visit: http://www.statistik.lmu.de/~leisch/Sweave/.

Dynamic report generation with knitr

What is R Markdown?

R Markdown is the integration of plain R code and Markdown, and is based on the knitr package and the open-source document converter, pandoc. It further combines dynamic documents, literate programming, and reproducible research. With the help of R Markdown, you can easily use R code and Markdown to create a report with human-readable documentations along with the results of your code. As an output option, you can choose between an HTML file, PDF, Microsoft Word, ioslides, and others.

A side note about LaTeX

LaTeX is an important component of R Markdown, therefore, the following are some notes about this technology: