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Welcome to the EpiEstim wiki!
EpiEstim is a method and set of software pieces to estimate the instantaneous reproduction number Rt in real time during epidemics.
The underlying methods are described in two publications:
- Cori A., et al. (2013). A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics, American Journal of Epidemiology, 178(9):1505–1512. https://doi.org/10.1093/aje/kwt133
- Thompson, R. N., et al. (2019). Improved inference of time-varying reproduction numbers during infectious disease outbreaks. Epidemics, 29, [100356]. https://doi.org/10.1016/j.epidem.2019.100356
The methods are implemented in the following pieces of software:
- R package
EpiEstim, available on Github and on CRAN - Web application
- Excel spreadsheet
estimate_R produces Bayesian estimates of R so depend on the data but also on the prior chosen (see here and here for details of the method). By default in estimate_R the prior is set to a mean of 5 and a standard deviation of 5. You can change these settings using the function make_config. It is recommended to check whether changing the prior dramatically affects the estimates, to assess whether results are primarily driven by the data or not.
At the moment EpiEstim only allows estimation of R using the same time unit for the incidence and the serial interval data. If you want to estimate R from weekly incidence data, you will therefore have to specify the distribution of the serial interval with week as the time unit.