This web application generates an estimate of infectious disease transmissibility throughout an outbreak. The time-dependent reproduction number (R) is inferred from disease incidence time series and patient data or estimates of the serial interval. For more information about how to use this application, please see the wiki. For the most part, we assume that users will want to upload their own data, however there are also some example datasets built in, to illustrate how the application might be used.
For more information on uploading your own data and on the required format of the data, please click here.
The authors request users to cite the original publication when referring to this tool, any results generated from it, or the R software application on which this tool is based (EpiEstim 2):
Thompson RN, Stockwin JE, van Gaalen RD, Polonsky JA, et al. Improved inference of time-varying reproduction numbers during infectious disease outbreaks. Epidemics (2019).