fvalka / covid19-austria-excess-mortality

Age structured model for estimation of excess mortality during the covid19 pandemic in Austria.

Excess Mortality During the COVID-19 Pandemic Period in Austria

Code for estimates of the excess mortality in Austria during the pandemic. Estimated using an age structured Bayesian generalized additive model, considering yearly trends and weekly seasonality.

Project Structure

The implementation is written in R using brms.

• data Input data files (most inputs are automatically downloaded in the pipline though)
• R All code

Building

Builds are executed by first installing the renv package and installing all required packages:

renv::restore()

Ensure that no build is skipped in the _targets.R file, all tar_cue_skip cues should look like this:

cue = tarchetypes::tar_cue_skip(FALSE)

Once all packages have been installed the targets pipeline can be executed using

run.sh

or

targets::tar_make()

Reproducible Development Environment

A docker-compose file is provided in this project to ensure a reproducible development environment.

To run the rstudio server in docker first set a PASSWORD in the docker compose file and then execute the following command:

docker-compose -f docker-compose-rstudio.yml up