Reference Management in RMarkdown


David M. Miller, Sophia Z. Shalhout


September 12, 2020

Integrate your EndNote library into RMarkdown

Background And Overview

STEP 1 - Open EndNote

STEP 2 - Select Pertinent References

STEP 3 - Export References

STEP 4 - Change the File Extension

STEP 5 - Find the Citation Key of Interest

STEP 6 - Format the YAML

Citation Style

  • pandoc uses a Chicago author-date by default

  • If you desire another style, you can specify a CSL 1.0 style in the YAML, as seen here:

       title: "Sample Document" 
       output: html_document   
       bibliography: bibliography.bibtex  
       link-citations: yes
STEP 8 - Insert Citation of Interest
  • Now we can enter our citation by placing the citation key (here @RN2687) within square brackets in the desired location in your text

STEP 9 - Add References
  • References will be placed at the end of your document, so make the last test in your RMarkdown # References

STEP 10 - Knit Your Document
  • Lastly, knit your document and you should see your desired references

Take Home Points

  • Coupling RMarkdown with a reference managing software is a great way to maximize your manuscript-generating efficiency

As always, please reach out to us with thoughts and feedback