Getting things set up for writing a reproducible scientific manuscript with R markdown  (CC060)
Channel: Riffomonas Project
Date: 2021-01-04

Most biologists write their manuscripts in a word processor like Microsoft Word. To maximize the reproducibility of your work, you should check out R markdown, which allows you to embed R code in your text. In this episode we'll see how set things up.

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. Proponents think that they should supplant operational taxonomic units (OTUs). What do you think? Pat demonstrates these concepts by live coding at the command line interface using GitHub Flow, Make, and RStudio.

0:00 Introduction
1:31 R markdown
4:48 Producing different types of output
12:04 Changing the aesthetics of a PDF 
17:57 Creating a cover page
25:49 Creating a make rule to render document
28:00 Brief word about Word files
29:25 Conclusion

The accompanying blog post contains the exercises and solutions can be found at http://www.riffomonas.org/code_club/2020-01-04-cover-page