1.1 What does this infrastructure do?

This infrastructure provides an automated data pipeline that gathers publicly available data on COVID-19 cases, deaths, tests, as well as on Variants of Interest/Concerns (VoI / VoC) and vaccination by country, and provides a weekly assessment of COVID-19 dynamics and levels of risks. The pipeline is implemented as a reportfactory which simplifies the handling of dependencies, data and scripts, and enables the compilation of analysis reports stored locally in dedicated, time-stamped folders.

A series of Rmd reports performs data gathering, various analysis, and produce the following information products:

• png figures (pinplots and tadpoles) summarising the dynamics per WHO region, stored on github and visible on the README.md page (i.e. landing page of the repository)

• rds files containing the results for each WHO region, also stored on github, which can then be used for further investigation or for interactive dashboards (e.g. shiny apps); some of these analyses are computer-intensive and would not be readily available on dashboards otherwise

• automated emails to a specific list of recipients providing a detailed report of countries classified into epidemiological risk levels based on incidence, growth and trend changes; this latter part is not stored on github