Computational protocol to perform a spatiotemporal reconstruction of an epidemic

Riccardo Nodari; Matteo Perini; Luca Fois; Lodovico Sterzi; Ester Luconi; Folco Vaglienti; Claudio Bandi; Elia Biganzoli; Massimo Galli; Francesco Comandatore

doi:10.1016/j.xpro.2023.102548

Computational protocol to perform a spatiotemporal reconstruction of an epidemic

STAR Protoc. 2023 Dec 15;4(4):102548. doi: 10.1016/j.xpro.2023.102548. Epub 2023 Sep 16.

Authors

Affiliations

¹ Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy. Electronic address: riccardo.nodari@unimi.it.
² Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy; Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA.
³ Department of Humanities, Section of Historical and Geographical Science, University of Pavia, Pavia, Italy.
⁴ Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.
⁵ Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy.
⁶ Department of Historical Studies, University of Milan, Milan, Italy.
⁷ Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biosciences, University of Milan, Milan, Italy.
⁸ Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy. Electronic address: francesco.comandatore@unimi.it.

Abstract

Here, we present a computational protocol to perform a spatiotemporal reconstruction of an epidemic. We describe steps for using epidemiological data to depict how the epidemic changes over time and for employing clustering analysis to group geographical units that exhibit similar temporal epidemic progression. We then detail procedures for analyzing the temporal and spatial dynamics of the epidemic within each cluster. This protocol has been developed to be used on historical data but could also be applied to modern epidemiological data. For complete details on the use and execution of this protocol, please refer to Galli et al. (2023).¹.

Keywords: Bioinformatics; Computer Sciences; Health Sciences.

MeSH terms

Cluster Analysis*