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The Epidemiologist R Handbook, a new open source public health resource

The Epidemiologist R Handbook, a new open source public health resource
Neale Batra image

Neale Batra @nsbatra

Founder, The Epidemiologist R Handbook
Mala Kumar image

Mala Kumar @malakumar85

Director of Tech for Social Good, GitHub Social Impact

August 16, 2021 // Tech for Social GoodOpen Source for Good

Published on: August 16, 2021

COVID-19 has put a global spotlight on epidemiology — a field in public health that looks at the spread of disease — and has galvanized our community to improve the technological tools that epidemiologists use on a daily basis. The Epidemiologist R Handbook is a grassroots effort hosted on GitHub to document and strengthen epidemiological data practices that use R, a popular open source programming language used in public health emergency settings. R can help users manage and connect a vast constellation of health-related data, forecast trends, analyze surveys, and rapidly produce customized figures, reports, and dashboards to inform decision-making. Since launching in May 2021, the handbook has been viewed 350,000 times by 55,000 people in 203 countries and territories.

According to Dr. Olivier Le Polain, the lead for COVID-19 analytics at the World Health Organization (WHO) Health Emergencies Programme,

The Epidemiologist R Handbook has already become a vital resource for epidemiologists around the world and will help strengthen public health analytics in emergency response.

Twitter users working in health and data science have also noted that the handbook is a valuable resource for epidemiologists and broader public health communities.

Tweet from Dr Ahmad Suleiman Idris A tweet from Dr Ahmad Suleiman Idris, a resident trainee in the Nigeria Field Epidemiology and Laboratory Training Programme

The Epidemiologist R Handbook is a free digital resource that can be downloaded for offline use. Readers can quickly find snippets of best-practice example code, or work step-by-step through tutorials using example data. It begins with R fundamentals and proceeds through an exhaustive list of topics, including data cleaning, analytics, visualization for epidemic response, making maps and dashboards, and automation of reports. It also provides guidance for people looking to transition to R from other software, like SAS, Stata, SPSS, and Excel.

Fifty epidemiologists from around the world have contributed to the handbook, drawing on their experience with organizations including WHO and Doctors Without Borders. Volunteer epidemiologists have started Spanish, French, Portuguese, Vietnamese, Simplified Chinese, Japanese, Turkish, and Mongolian translations of the handbook, as well.

Contributing to the Epidemiologist R Handbook

Public health practitioners have labored tirelessly to contain epidemics and inform the public of the latest developments. The Epidemiologist R Handbook is a force for change: to support and unify the vast network of applied epidemiologists around the world.

Currently, GitHub Tech for Social Good’s Skills-Based Volunteering program provides the handbook project with technical support, including adopting git best practices and setting up automated workflows with GitHub Actions. According to Bassem Dghaidi (@link-), the GitHub volunteer on the project,

The Epi R Handbook is an ‘open source unicorn’ in that it received immediate recognition by the community. It’s very well polished. It has been a privilege to connect with its maintainers and share the experience of GitHub’s Professional Services team to make the handbook as impactful as possible!

The handbook is written in R markdown and is produced using the bookdown R package. If you’re interested in contributing content or assisting with translation, please contact the team at Technical comments can be logged in GitHub repository Issues.

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