This Repository contains python and web scripts to estimate the effective reproduction number R of SARS-CoV 2 (the virus causing COVID-19) for various countries over time.
The easiest way to use these scripts is by pointing your web browser to the online version:
That said, you are very welcome experiment with this data yourself. The easiest version to do so is to use the python version of the scripts. In this context, we assume that you are using a non-ancient Linux distribution which has Python3 and git installed. If you want to visualize the results, having gnuplot installed is highly advised, although you can inspect and process the results using any modern spreadsheet program.
First, you need to clone or update the source data from Johns Hopkins University:
./updateData.sh
For most countries, you can then extract the curve of the estimated effective reproduction number like this:
COUNTRY="Germany"
./estimateR.py "$COUNTRY" > "r-estimate-$COUNTRY.csv"
The result is contained in the file "r-estimate-$COUNTRY.csv" which
can be inspected via a spreadsheet program or visualized using tools
like gnuplot. To simplify the latter, a small shell script is
provided:
COUNTRY="Germany"
./estimateAndVisualizeR.sh "$COUNTRY"
If you want to deploy the interactive version on your own web server, you need to have the npm package manager installed. Then, run
./extractAllCountries.sh
npm install
./collectHtmlDependencies.sh
The results are contained in the 'html' subdirectory. To deploy it, copy it somewhere to your webserver. Any webserver which is able to serve static files will do.
Adding a new JavaScript dependency can be achieved like this:
- Adapt
package.json - Run
npm install - Use it in the
.htmland.jsfiles - Adapt
collectHtmlDependencies.sh
- Background article: https://medium.com/@tomaspueyo/coronavirus-act-today-or-people-will-die-f4d3d9cd99ca
- Awesome Resources on COVID-19: https://github.com/soroushchehresa/awesome-coronavirus#awesome-coronavirus----
- CCC's collection of information resources: https://github.com/cwoomi/cert-covid19#dashboards