Facilitating Reproducibility and Collaboration with Literate Programming

Abstract

A fundamental challenge for open science is how best to create and share documents containing computational results. Traditional methods involve maintaining the code, generated tables and figures, and text as separate files and manually assembling them into a finished document. As projects grow in complexity, this approach can lead to procedures which are error prone and hard to replicate. Fortunately, new tools are emerging to address this problem and librarians who provide data services are ideally positioned to provide training. In the workshop we’ll use RStudio to demonstrate how to create a “compilable” document containing all the text elements (including bibliography), as well as the code required to create embedded graphs and tables. We’ll demonstrate how the process facilitates making revisions when, for example, a reviewer has suggested a revision or when there has been a change in the underlying data. We’ll also demonstrate the convenience of integrating version control into the workflow using RStudio’s built-in support for git. Slides and exercises are available at https://hdekk.github.io/escience2018/.