epicontacts: Handling, visualisation and analysis of epidemiological contacts [version 2; peer review: 2 approved, 1 approved with reservations]
VP Nagraj,
Nistara Randhawa,
Finlay Campbell,
Thomas Crellen,
Bertrand Sudre,
Thibaut Jombart
Affiliations
VP Nagraj
Research Computing, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA
Nistara Randhawa
One Health Institute, University of California, Davis, Davis, CA, 95616, USA
Finlay Campbell
MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W2 1PG, UK
Thomas Crellen
Mahidol-Oxford Tropical Medicine Research Unit, Bangkok , 10400, Thailand
Bertrand Sudre
European Centre for Disease Prevention and Control, Stockholm, Sweden
Thibaut Jombart
MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W2 1PG, UK
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.
