Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland

Here lives the code and data for Chen, Chaoran, et al. "Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland." Epidemics (2021); doi: 10.1016/j.epidem.2021.100480.

Zenodo archive of this repository: 10.5281/zenodo.7979278

Our website gives a concise description about the data and puts the figures into context.

This repository was updated between mid-January and mid-April 2021. For newer information, please visit CoV-Spectrum.

Program

Overview

The analysis is performed in two steps by different sub-programs. In the first step, taking the overall number of reported cases and the results from sequencing, the code/analysis_and_plots.py script estimates the advantage of the variant and creates plots of the estimated proportion and cases through time under different assumptions. The generated plots are stored in figures/. Further, the script estimates the number of absolute cases of the variant and writes them into code/Re/data/. Then, in the second step, the code/Re/estimate_Re.R script takes the computed values from code/Re/data/ and estimates the Re. The resulting values and plots are stored in code/Re/figures/.

Usage

Install Dependencies

• Python and the packages defined in code/requirements.txt
• R and the packages tidyverse, lubridate, viridis, EpiEstim
• Further, this program requires the shiny-dailyRe project. Please clone that repository and install its dependencies.

Run

1. Run analysis_and_plots.py. It does not need further configurations.
2. Open code/Re/estimate_Re.R and set the app_dir variable to the path of the cloned shiny-dailyRe repository.
3. Run estimate_Re.R