Reproducible Research in R

Ilya Kashnitsky

14 December 2016

Reproducible research

Reproducibility

Reproducibility of scientific results is the main challenge of the modern academia
Collaboration, Open Science (2015). Estimating the reproducibility of psychological science. Science, 349(6251), aac4716. https://doi.org/10.1126/science.aac4716
Out of 100 papers only 39 were replicated

Literate programming

The idea of literate programming dates back to mid-80s
The core idea: code, comments, and results should appear together in one document.

Peng, R. D. (2011). Reproducible Research in Computational. Science, 334(6060), 1226â€“1227. https://doi.org/10.1126/science.1213847

peng

markdown

What is markdown?

Markdown is a lightweight markup language with plain text formatting syntax designed so that it can be converted to HTML and many other formats using a tool by the same name.

Where is it used?

Everywhere

Reddit
StackOverflow
github
Publons
Habrahabr
…

The basics of markdown

Basically, everything is just plain text unless modified
Be careful. There are n+1 versions of markdown.
The most popular are: GFM, rmarkdown and pandoc

http://rmarkdown.rstudio.com/authoring_basics.html

Task

Create a webpage using markdown.
Use as many markdown options as you can think of. Include image, gif, video, link…

http://txti.es
10 minutes

The author of txti, Barry T. Smith, is a great advocate of lightweight websites
http://motherfuckingwebsite.com

rmarkdown

http://rmarkdown.rstudio.com

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

R notebooks

The recently presented v1.0 version of RStudio brings R-notebooks as on of the main features.
This type of document implements the principles of literate programming.

http://www.danielwells.me/human-lifespan-limit/