https://github.com/contactmodel/COVID19-Japan-Reff

https://github.com/contactmodel/COVID19-Japan-Reff

Last synced: about 2 months ago
JSON representation

• Host: GitHub
• URL: https://github.com/contactmodel/COVID19-Japan-Reff
• Owner: contactmodel
• Created: 2020-05-11T13:00:02.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2021-12-19T10:54:25.000Z (almost 3 years ago)
• Last Synced: 2024-07-04T00:56:18.890Z (3 months ago)
• Language: Jupyter Notebook
• Size: 2.9 MB
• Stars: 217
• Watchers: 32
• Forks: 35
• Open Issues: 5
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# 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](https://nbviewer.jupyter.org/github/contactmodel/COVID19-Japan-Reff/blob/master/scripts/A.%20Showing%20the%20epidemic%20curve.ipynb?flush_cache=true)

**Main analysis**

* [B. Calculation of Rt using Maximum likelihood estimation.ipynb](https://nbviewer.org/github/contactmodel/COVID19-Japan-Reff/blob/master/scripts/B.%20Calculating%20Rt%20using%20Maximum%20likelihood%20estimation.ipynb)

* [C. Calculating the Rt in Stan.ipynb](https://nbviewer.org/github/contactmodel/COVID19-Japan-Reff/blob/master/scripts/C.%20Calculating%20the%20Rt%20in%20RStan.ipynb) (Stan script can be found [here](https://github.com/contactmodel/COVID19-Japan-Reff/blob/master/scripts/fit_infection.stan))

------

**Thank you for your interest to our work.**