This repository contains the scripts used to analyzed the data reported in draft:

covid19census: U.S. and Italy COVID-19 epidemiological data and demographic and health related metrics

Claudio Zanettini*, Mohamed Omar*, Wikum Dinalankara, Eddie Luidy Imada, Elizabeth Colantuoni, Giovanni Parmigiani, and Luigi Marchionni.

Files and folders:

code

Contains the scripts for retrieving, pre-processing and analyzing the data.

• code/libraries_functions: loads the libraries (including covid19census).

• code/functions_analysis: contains functions used to pre-process, analyze and summarize data. Functions are documented.

• code/us_preprocess: this is used to retrieve and pre-process U.S data. Execution of this script returns the dataframe used for the analyses (dat_selected). A static copy of the dataframe is in data/all_raw.RDS.

• code/stratified_analysis.R: it executes all the scripts and perform stratified analyses.

data

• diabetes_confounders.R: list of confounders selected for analysis.

objs

• dat_diab.RDS: data used for the analysis.

• MRR_stata_diab_5.RDS: table of results of the regression.

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Sources and data

The file data/all_raw.RDS contains a static copy of the data used for the analysis.

Details regarding the data sources as well as functions to extract updated COVID-19 data and aggregate them with other socio-economic and health related metrics can be found in the covid19census R package. Please refer to the package README or documentation for more information regarding the variables. The scripts used to import static data are reported in the package repository here.

Note: use package renv and renv.lock file in parent folder to install the same versions of packages that we used.