Integrating text, code, and output with R markdown: a game changer for reproducibility (CC030)
Channel: Riffomonas Project
Date: 2020-09-14

In this screencast tutorial, Pat Schloss shows how you can use R markdown to improve the reproducibility of a data analysis by refactoring an R script developed in a previous episode. We'll also use R markdown to automatically insert the version number for the packages we're using in this project into our README file. This episode is part of a larger arc of episodes investigating the sensitivity and specificity of amplicon sequence variants (ASVs), also known as exact sequence variants (ESVs). ASVs are growing in popularity for analyzing microbial communities using 16S rRNA gene sequences. Pat demonstrates these concepts by live coding at the command line interface using RStudio, GitHub Flow, and make.

The accompanying blog post contains the exercises and solutions can be found at http://www.riffomonas.org/code_club/2020-09-14-rmarkdown.