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As field epidemiologists around the world continue to respond to the COVID-19 pandemic, we are seeing a greater demand for tools, resources and training needed to better understand the abundance of data being collected every day. While many epidemiologists are trained in analytic software like SAS, STATA, and SPSS, some find these platforms to be cost prohibitive and time-consuming when dealing with large-scale outbreaks. 

In recent years, many public health professionals have begun using R for data analysis, reporting and management because it is free, open-source and offers high-quality data visualizations. The software’s ability to automate epidemiological reports is especially useful for the COVID-19 pandemic as it allows for information to be analyzed and shared at the faster pace needed for outbreak response. In August 2020, the EPIET Alumni Network (EAN) was awarded a TEPHINET COVID-19 Emergency Capacity Building Grant to develop an Epi R handbook catered to field epidemiologists responding to the pandemic. With these funds, EAN coordinated the creation of a free, open-source R reference manual. 

The handbook was a collaborative effort produced by epidemiologists from around the world, including graduates and trainees of Field Epidemiology Training Programs (FETPs), drawing upon experiences in local, national, academic and emergency settings. 

This free, open source reference manual provides sample R code and brief tutorials addressing common data management and visualization tasks with epidemiological examples. Its opening pages cover R fundamentals and assist with the transition to R from other software such as SAS, Stata, SPSS, or Excel. Subsequent pages address core data cleaning skills; descriptive and analytical approaches to linelist, survey, survival, contact tracing, time series, and geospatial data; creation of dashboards and automation of reports; how to generate figures such as epidemic curves, transmission chains, demographic pyramids, and phylogenetic trees; as well as basic epidemic modeling and other topics.

Click here to access the Epi R Handbook.

The authors are grateful to the dozens of contributors and supporting organizations that made the Epi R Handbook possible, including the EPIET Alumni Network (EAN),  Médecins Sans Frontières (MSF) Operational Centre Amsterdam (OCA), and TEPHINET.

 Please note that references herein to the R software do not necessarily constitute or imply its endorsement or recommendation by TEPHINET.