R for applied epidemiology and public health

This handbook strives to:

  • Serve as a quick R code reference manual
  • Provide task-centered examples addressing common epidemiological problems
  • Assist epidemiologists transitioning to R
  • Be accessible in settings with low internet-connectivity via an offline version


 

Written by epidemiologists, for epidemiologists

We are applied epis from around the world, writing in our spare time to offer this resource to the community. Your encouragement and feedback is most welcome:

How to use this handbook

  • Browse the pages in the Table of Contents, or use the search box
  • Click the “copy” icons to copy code
  • You can follow-along with the example data
  • See the “Resources” section of each page for further material

Offline version

See instructions in the Download handbook and data page.

Languages

We want to translate this into languages other than English. If you can help, please contact us.

Acknowledgements

This handbook is produced by a collaboration of epidemiologists from around the world drawing upon experience with organizations including local, state, provincial, and national health agencies, the World Health Organization (WHO), Médecins Sans Frontières / Doctors without Borders (MSF), hospital systems, and academic institutions.

This handbook is not an approved product of any specific organization. Although we strive for accuracy, we provide no guarantee of the content in this book.

Contributors

Editor: Neale Batra

Project core team: Neale Batra, Alex Spina, Amrish Baidjoe, Pat Keating, Henry Laurenson-Schafer, Finlay Campbell, Paula Blomquist, Aminata Ndiaye, Isaac Florence, Isha Berry, Mathilde Mousset, Sara Hollis, Liza Coyer, Kate Kelsey, Marie-Amélie Degail Chabrat, Joao Muianga

Authors: Neale Batra, Alex Spina, Paula Blomquist, Finlay Campbell, Henry Laurenson-Schafer, Isaac Florence, Natalie Fischer, Aminata Ndiaye, Liza Coyer, Jonathan Polonsky, Yurie Izawa, Chris Bailey, Daniel Molling, Isha Berry, Emma Buajitti, Mathilde Mousset, Sara Hollis, Wen Lin

Reviewers: Pat Keating, Annick Lenglet, Margot Charette, Danielly Xavier, Esther Kukielka, Michelle Sloan, Aybüke Koyuncu, Rachel Burke, Kate Kelsey, Berhe Etsay, John Rossow, Mackenzie Zendt, James Wright, Laura Haskins, Flavio Finger, Tim Taylor, Jae Hyoung Tim Lee, Brianna Bradley, Wayne Enanoria, Manual Albela Miranda, Molly Mantus, Pattama Ulrich, Joseph Timothy, Adam Vaughan, Olivia Varsaneux, Lionel Monteiro, Joao Muianga

Illustrations: Calder Fong

Funding and support

The handbook received supportive funding via a COVID-19 emergency capacity-building grant from TEPHINET, the global network of Field Epidemiology Training Programs (FETPs).

Administrative support was provided by the EPIET Alumni Network (EAN), with special thanks to Annika Wendland. EPIET is the European Programme for Intervention Epidemiology Training.

Special thanks to Médecins Sans Frontières (MSF) Operational Centre Amsterdam (OCA) for their support during the development of this handbook.

This publication was supported by Cooperative Agreement number NU2GGH001873, funded by the Centers for Disease Control and Prevention through TEPHINET, a program of The Task Force for Global Health. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the Centers for Disease Control and Prevention, the Department of Health and Human Services, The Task Force for Global Health, Inc. or TEPHINET.

Inspiration

The multitude of tutorials and vignettes that provided knowledge for development of handbook content are credited within their respective pages.

More generally, the following sources provided inspiration for this handbook:
The “R4Epis” project (a collaboration between MSF and RECON)
R Epidemics Consortium (RECON)
R for Data Science book (R4DS)
bookdown: Authoring Books and Technical Documents with R Markdown
Netlify hosts this website

Terms of Use and Contribution

License

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

Academic courses and epidemiologist training programs are welcome to use this handbook with their students. If you have questions about your intended use, email .

Citation

Batra, Neale, et al. The Epidemiologist R Handbook. 2021. DOI

Contribution

If you would like to make a content contribution, please contact with us first via Github issues or by email. We are implementing a schedule for updates and are creating a contributor guide.

Please note that the epiRhandbook project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.