Analysis of excess mortality in Italy during the COVID-19 pandemic

This repository stores the R code, data, and full results presented in the article:

Scortichini M, Schneider dos Santos R, De' Donato F, De Sario M, Michelozzi P, Davoli M, Masselot P, Sera F, Gasparrini A. Excess mortality during the COVID-19 outbreak in Italy: a two-stage interrupted time series analysis. International Journal of Epidemiology. 2020;49(6):1909.1917. DOI: 10.1093/ije/dyaa169 [freely available here]

The work was supported by the Medical Research Council-UK (Grant ID: MR/M022625/1) and the European Union’s Horizon 2020 Project Exhaustion (Grant ID: 820655).

The full set of results, including number and fraction of excess deaths (with 95%eCI) by geographical aggregation (provinces, region, and full country), sex, age groups, and period (15th of February - 15th of May 2020, and then by week starting from the 1st of February) is provided in the output folder of this repository.

A Shiny app (still under development) to visualize the results in maps and other graphs is available here.

The R scripts in this repository can be used to fully replicate the analysis and results illustrated in the article. The code can be used to download the original data from this webpage in the ISTAT website (update of 18 June), and then to perform all the steps of the analysis. The scripts are expected to be run in their order. Specifically:

• 00.pkg.R loads the R packages
• 01.prepdatafull.R downloads and unzip the data in the folder data, and prepares the dataset by reshaping it, creating time variables, and ordering
• 02.param.R defines the sub-groups and the modelling parameters for the analysis
• 03.prepdatamodel.R creates the final dataset by selecting the data and aggregating province-specific series
• 04.model.R runs the two-stage model
• 05.showexample.R illustrates how to extract the main results and produce a map
• 06.storeall.R performs the analysis for all the combinations of geographical area, sex, and age group, and stores them in arrays
• 07.showmain.R shows the estimates reported in the paper
• 08.showadd.R shows additional results
• 09.tables.R produces the tables of the article and store them in the folder tables
• 10.plots.R produces the graphs included in the article and store them in the folder graphs
• 11.output.R produces the final output of the analysis as excel files with all the estimates and store them in the folder output
• 12.otherplot.R produces other graphs