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R Demonstration for Emory COVID-19 Response Collaborative

This website hosts training materials for the R demonstrations first delivered by Applied Epi to 40 Rollins COVID-19 Epidemiology fellows and colleagues from the Emory COVID-19 Response Collaborative in August 2021.
Links to the video recordings are available below and on our YouTube channel.

Applied Epi

Applied Epi is the non-profit organization that wrote the Epidemiologist R Handbook, a free R reference manual for applied epidemiology and public health which has been used by 50,000 people around the world.

Contact contact@appliedepi.org to schedule R demonstrations, interactive training sessions, Intro-to-R workshops, or to subscribe to “help desk” support services from R experts who know applied epi!

The Emory COVID-19 Response Collaborative

The Emory COVID-19 Response Collaborative is an initiative led by the Emory Rollins School of Public Health in collaboration with the Georgia Department of Public Health (GDPH). Its mission is to provide academic support to state and local health department partners during the COVID-19 crisis. One of its seminal programs is the Rollins Epidemiology Fellows Program, a 2-year fellowship designed to attract, place and support early-career epidemiologists across Georgia’s 18 health districts and GDPH. With assistance from ECRC leadership and the Fulton County Board of Health, Applied Epi designed this tailored training session to build the fellows’ analytic capabilities in R through examples tailored to their applied needs in preparing jurisdictional COVID-19 outbreak reports and maps.

Training materials

The links below contain all of the materials used for the course. See our Github repository for more detail:

• Agenda

Session 1: Case study walk-through - data cleaning and analytic workflow in an R markdown report

• Analytical workflow presentation slides
• Case study R project (zip download of example data and R markdown script)

Session 2: Data visualization with ggplot2

• Data visualization presentation slides
• R markdown script

Please note that all these training materials use fake example data in which no person is identifiable and the actual values have been scrambled.

Video recordings

Session 1: Data cleaning and analytic workflow (13^th August 2021)

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Session 2: Data visualization with ggplot (20^th August 2021)

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Acknowledgements

Instructors and authors from Applied Epi included:

• Neale Batra
• Alex Spina
• Henry Laurenson-Schafer
• Mathilde Mousset
• Wen Lin

Many thanks to the Fulton County Board of Health, that provided example data (anonymized and scrambled) for the case study.

Representatives from the Emory COVID-19 Response Collaborative included:

• Zena Belay
• Dr. Allison Chamberlain
• Shelby Rentmeester
• Eve Rose

Terms of Use and 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 material with their students. If you have questions about your intended use, email contact@appliedepi.org.

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 Epi R Handbook project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.