Preprint

Epilocal: a real-time tool for local epidemic monitoring

Bonetti, M., Basellini, U.
arXiv e-prints (COVID-19 e-print) 2003.07928
8 pages.
arXiv
submitted on: 17 March 2020; last revised: 21 April 2020 (v3) (2020), unpublished
Open Access
Reproducible

Abstract

We describe Epilocal, a simple R program designed to automatically download the most recent data on reported infected SARS-CoV-2 cases for all Italian provinces and regions, and to provide a simple descriptive analysis. For each province the cumulative number of reported infected cases is available each day. In addition, the current numbers of hospitalized patients (separately for intensive care or not) and the cumulative number of deceased individuals are available at the region level. The data are analyzed through Poisson generalized linear models with logarithmic link function and polynomial regression on time. For cumulative data, we also consider a logistic parameterisation of the hazard function. Automatic model selection is performed to choose among the different model specifications, based on the statistical significance of the corresponding estimated parameters and on goodness-of-fit assessment. The chosen model is used to produce up-to-today estimates of the growth rate of the counts. Results are plotted on a map of the country to allow for a visual assessment of the geographic distribution of the areas with differential prevalence and rates of growth.

Keywords: Italy, epidemics, mortality
The Max Planck Institute for Demographic Research (MPIDR) in Rostock is one of the leading demographic research centers in the world. It's part of the Max Planck Society, the internationally renowned German research society.