Real-time estimation of the effective reproduction number of COVID-19 in Japan

Code scripts used for simulations Sung-mok Jung, Andrei R. Akhmetzhanov, Kenji Mizumoto, Hiroshi Nishiura

Data used for simulations is available in the data-folder. The simulations were done using R (version 4.0). The results can be found in the results-folder.

Scripts

Representing the data

• A. Showing the epidemic curve.ipynb

Main analysis

• B. Calculation of Rt using Maximum likelihood estimation.ipynb
• C. Calculating the Rt in Stan.ipynb (Stan script can be found here)

Thank you for your interest to our work.