Covid-19 incidence per week by community
This repository is meant to compute and display the population-normalized Covid-19 incidence for each community (Gemeinde) in Breisgau-Hochschwarzwald per week. Only limited data is available, since it's published weekly as a PDF and previous week's data removed. GIS data is from ESRI Deutschland and © GeoBasis-DE / BKG 2016.
Last week:
Animation:
Caveats
There are a few things that should be kept in mind when looking at this. Firstly, many of the communities are quite small, so a single case will mean that their population-normalized incidence will increase by ~40 cases/100,000 population/week. A second main caveat is that these numbers are approximate. I don't have access to the actual weekly numbers, so things like corrections to a previous week's values will either get lost or artificially decrease the numbers for the week during which the correction is reported.
Data harvesting
Data is extracted from the PDF produced by the Landesregierung Breisgau-Hochschwarzwald every week using pdftotext. Then the scripts under scripts/ are used to format this into a standard TSV file (incidence.txt). The text file made from the PDF isn't always formatted exactly the same from week to week, so the python scripts used for this often need to be tweaked slightly.
Image creation
The TSV data is loaded into R and the final animated GIF created using ggplot2, gganimate, sf and gifski.