2/28/2021

R For Reproducible Research

to err is human,

we can ONLY detect and correct any error, if the source code is readily available.

The session is ONLY for honest human beings

Markdown

  • Markdown is a standard for writing in plain text then producing formatted output.

  • Markdown produces dozens of static and dynamic output formats including

    • PDF,

    • MS Word, PPT,

    • HTML5 slides,

    • books, scientific articles,

    • and more.

Markdown = reproducible research

  • The structure of a Markdown document is concrete and transparent.

    • A productive interface weaves together narrative text and code to produce elegantly formatted output.

  • The work flow is fully reproducible

Markdown = The Future

  • portable: Files can be opened using any application.

  • platform independent: You can use it on any device running any operating system.

  • future proof. Even if the application you’re using stops working at some point in the future, you’ll still be able to fully use the files.

    • This is critical when it comes to books, university theses, and other milestone documents that need to be preserved indefinitely.

Kicking the Tires

The best way to get started with Markdown is to use it.

Structure

  • metadata

  • Text

  • Code

Frameworks

R Markdown reports rely on three frameworks

  1. YAML for metadata

  2. markdown for text

  3. knitr for code

Demo

DIY workshop