SEPIA epidemiological model

The MATLAB® code in this repository runs the SEPIA epidemiological model and reproduces the scenarios shown in figure 2 and S1 of the manuscript

The geography of COVID-19 spread in Italy and implications for the relaxation of confinement measures

Enrico Bertuzzo, Lorenzo Mari, Damiano Pasetto, Stefano Miccoli, Renato Casagrandi, Marino Gatto, Andrea Rinaldo

medRxiv 2020.04.30.20083568; doi:10.1101/2020.04.30.20083568

Now published in Nature Communications

• Bertuzzo, E., Mari, L., Pasetto, D. et al. The geography of COVID-19 spread in Italy and implications for the relaxation of confinement measures. Nat Commun 11, 4264 (2020). doi:10.1038/s41467-020-18050-2

Citation in RIS format.

Running instructions

Launch SEPIA_main.m to run the model. The code reads the data and a sample of the posterior distribution of parameters and runs the model producing the two figures contained in the folder Expected_Results.

To produce different scenarios, the user can change the parameter betaInc (line 108 of SEPIA_main.m). Figure 2 and S1 of the preprint have been obtained using betaInc=1, betaInc=1.2 and betaInc=1.4.

The code runs 2000 realizations of the model and takes less than a minute in a standard laptop or desktop computer. To obtain a more robust and smoother estimation of the probability distribution of the output, the user can increase the number of posterior samples used (parameter NSample, line 102 of SEPIA_main.m).

The code has been tested on MATLAB versions R2018a and R2019b.