COVID19-Rt

Code to calculate time-varying effective reproduction number (Rt), case rate, and death rate for COVID-19.

Structure of Code

• pois_reg_estimates: Implements our new Poisson regression-based method, as described in our preprint.
• initial_estimates: Initial Rt estimates calculated using EpiEstim (Cori, A., et al., 2013)
• helpers: Helper functions.
• preprocess_data: Code for preprocessing the data.
• sens_analysis: Sensitivity analysis

Obtaining Rt Estimates

Within pois_reg_estimates and initial_estimates is a README with links to the latest Rt estimates.