Chapter 1 Introduction

Welcome to this short handbook describing an outbreak dynamics surveillance system for COVID-19. This infrastructure was developed to provide weekly assessments of risk levels for different countries in relation to the countries’ overall levels of infection, epidemic growth, and indications of trend acceleration.

This infrastructure is written in R, and relies on the following key components:

• Rmarkdown (.Rmd) reports implementing the data gathering, preparation, analysis, and producing synthesis reports

• the reportfactory providing the backbone of the infrastructure

• a public github repository used for hosting files, version control, and automation through github actions