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Version 2. F1000Res. 2018 May 10 [revised 2018 Oct 11];7:566. doi: 10.12688/f1000research.14492.2. eCollection 2018.

epicontacts: Handling, visualisation and analysis of epidemiological contacts.

Author information

Research Computing, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA.
One Health Institute, University of California, Davis, Davis, CA, 95616, USA.
MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W2 1PG, UK.
Mahidol-Oxford Tropical Medicine Research Unit, Bangkok , 10400, Thailand.
European Centre for Disease Prevention and Control, Stockholm, Sweden.


Epidemiological outbreak data is often captured in line list and contact format to facilitate contact tracing for outbreak control. epicontacts is an R package that provides a unique data structure for combining these data into a single object in order to facilitate more efficient visualisation and analysis. The package incorporates interactive visualisation functionality as well as network analysis techniques. Originally developed as part of the Hackout3 event, it is now developed, maintained and featured as part of the R Epidemics Consortium (RECON). The package is available for download from the Comprehensive R Archive Network (CRAN) and GitHub.


R; contact tracing; outbreaks

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