EpiEstim is an R package used to estimate the time-varying reproduction number (Rₜ) from epidemic data. It calculates Rₜ using time series data of incident cases and the serial interval distribution. The package supports various methods for defining the serial interval, including fixed values and distributions based on data. It can analyze both daily and aggregated incidence data by reconstructing daily counts. EpiEstim is documented with functions for data input, estimation, and visualization, and is available through CRAN and GitHub