Subregional Estimates of Rt for Covid-19 in Brazil

City level estimates of the time-varying reproduction number of Covid-19 produced using EpiNow2 based on data from brazil.io. Regional estimates for Brazil (along with a national estimate) are available here. Detail of the method used is given here, though the estimates shown here were derived using an approximate approach (direct de-convolution of observed cases) rather than the exact method used on epiforecasts.io and therefore should be considered indicative. The code and data supporting these estimates is available here. Estimates are available in a summarised form here.

Data

• Rt estimates: data/rt/<date>/rt.csv

Dependencies

Install the required dependencies using:

devtools::install_dev_deps()

Updating

Run the following bash script to update the data, delay distributions and to estimate Rt for each area that fits the criteria specified in R/update-data.R.

bash bin/update.sh

See the bash script for links to each underlying script. On a 4 core computer reproducing these estimates should take approximately 5 hours.