Investigation and Visualization of the Time-Delays Inherent to the Estimation of the Time-Varying Reproduction Number R_t as Published for Austria

R shiny app to visualize and investigate the different time delays in the estimates of the time-varying reproduction number, which is currently being published for Austria.

The estimation of R_t is based upon the EpiEstim R package, which uses the method described in Cori, A., Ferguson, N. M., Fraser, C. & Cauchemez, S. A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics. American Journal of Epidemiology 178, 1505–1512 (2013).

The time-delay estimation is based upon published estimates and our own work. For further details please refer to the current draft of our method paper: Valka, F. & Schuler, C. Estimation and Interactive Visualization of the Time-Varying Reproduction Number Rt and the Time-Delay from Infection to Estimation. (2020).

Example Output

Available on the web at: covid19-r.com

Dataset Output

The Rt estimates are now also available as CSV files in the GitHub repo here in the folder: r_estimate/data/csv

for each time window, tau, using the naming schema {state}/r-estimate-{tau}.csv with AT being the countrywide estimate.

Build

The Shiny app can simply be built using the Dockerimage provided in this repo.

docker build . -t r-estimate

Run Shiny Server

Everything needed to run the shiny server and appis already prepared in the Dockerimage:

docker run -d -p 3838:3838 r-estimate

Updating Estimates

Updates are run by running estimates.R.

RScript estimates.R

Combined Time Delays for Specific Assumed Underlying Distributions

Rds-files of the time-delay ECDFs for Austria can be found in the r_estimate/data folder.

For obtaining your own estimates you can use the RScripts provided in time_delay_ecdf.

Data Sources

Case data for Austria

Bundesministerium für Soziales, Gesundheit, Pflege und Konsumentenschutz aggregated by the Complexity Science Hub Vienna and published on GitHub.

The data as published at the 15:00 CET deadline is used in this dataset.

AGES R_t estimate

TU Graz Rt,τ estimate AGES - Österreichische Agentur für Gesundheit und Ernährungssicherheit GmbH available online here: Epidemiologische Parameter des COVID19 Ausbruchs, Update 10.07.2020, Österreich, 2020

Public holidays

Public holiday data from nager-date is used for a different fill colour on public holidays.