Inserting references into R markdown documents for a scientific paper (CC072)
Channel: Riffomonas Project
Date: 2021-02-15

R markdown documents are great for reproducibility, but can you insert references like you would need for a scientific paper? YES! In this episode of Code Club, Pat Schloss will show you his process of inserting references into manuscripts that he writes using R markdown.

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) and operational taxonomic units (OTUs). 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.

The accompanying blog post can be found at http://www.riffomonas.org/code_club/2021-02-15-citations

You can also find complete tutorials for learning R with the tidyverse using...
Microbial ecology data: http://www.riffomonas.org/minimalR/
General data: http://www.riffomonas.org/generalR/

0:00  Introduction
2:33  Strategy for adding citations
6:53  references.bib & asm.csl files
9:50  Using google scholar to find bibtex-formatted references
12:44 Using EndNote to find bibtex-formatted references
14:05 Using PubMed to find bibtex-formatted references
16:04 Adding multiple references at the same location
21:22 Putting the references section in the correct location
23:25 Giving references a hanging indent
24:58 Cleaning up references
30:54 Conclusions