COVID-19 Dashboard

During the early pandemic there was a lack of COVID-19 related dashboards that unified German COVID-19 datasources. As such, this dashboard uses data from the German Interdisciplinary Association for Intensive Care and Emergency Medicine (DIVI) and the Robert Koch Institute (RKI).

This dashboard is available at shiny.bawki.de/covid

Open data sources

Intensive care registry

• JSON API with real time hospital data from https://www.intensivregister.de/api/public/intensivregister
• Daily DIVI report as csv from https://diviexchange.blob.core.windows.net/%24web/DIVI_Intensivregister_Auszug_pro_Landkreis.csv

RKI

• RKI report from https://www.arcgis.com/sharing/rest/content/items/f10774f1c63e40168479a1feb6c7ca74/data
• Historical RKI data from the arcgis REST API https://services7.arcgis.com/mOBPykOjAyBO2ZKk/arcgis/rest/services/rki_history_hubv/FeatureServer/0/query

Installation

Build the docker image

1. Download this repository git clone git@github.com:bogie/divi-dashboard.git
2. Generate a Mapbox Token from mapbox.com and save to

app/mapBoxToken

3. Build the docker image, make sure to substitute <image name> with your desired name for the image, I personally use bawki/divi-dashboard

sudo docker build -t <image name> .

Configuration

This dashboard uses a cron service to download new data at

• 04:00 GMT+1 from RKI sources
• 14:00 GMT+1 from DIVI sources

These times are chosen, because new data will be made available at ~ 03:00 and 11:30 GMT+1 respectively, sometimes uploads will be 1-2 hours delayed, therefore I use a generous buffer.

In order for data updates to work, you will need to setup a data folder on your device, which will be mounted/bound by the docker container.

1. Create the data directories

mkdir -p /srv/shiny/dashboard/data/rawData
mkdir -p /srv/shiny/dashboard/data/json_data
mkdir -p /srv/shiny/dashboard/data/rkiData

2. Copy or link the update scripts from the git folder

cd /srv/shiny/dashboard/
ln -s /path/to/app/updateRKI.R
ln -s /path/to/app/updateDIVIdata.R

3. make sure the folders are owned by the user, which will run the R scripts and has read/write access to the data folder
4. create cron jobs, run crontab -e as the aforementioned user

# Optional, to get notified each time any of the jobs are running
MAILTO=your@email.tld
0 14 * * * cd /srv/shiny/dashboard/data && Rscript updateDIVIdata.R
0 4 * * * cd /srv/shiny/dashboard/data && Rscript updateRKI.R

shinyproxy.io

This docker image is used in conjunction with shinyproxy.io, make sure you have a working instance and use the following entry in your application.yml.

specs:
  - id: dashboard
    display-name: divi dashboard
    description: Dashboard of RKI and DIVI data
    container-cmd: ["R","-e","shiny::runApp('/root/diviDashboard')"]
    container-image: <image name>
    container-volumes: ["/srv/shiny/dashboard/data:/root/diviDashboard/data"]
    user: "<UID>:<GID>"
    max-lifetime: -1
    heartbeat-timeout: -1

Make sure you substitute <UID> and <GID> as the data user ids, and <image name> with the build name you used earlier to build the docker image.