covid19 and influenza vaccination coverage

This repository contains the scripts used to analyze the data reported in the paper:

Influenza Vaccination and COVID-19 Mortality in the USA: an ecological study

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

Files and folders:

/code

• code/analysis.R: it executes all the the scripts in /code/scripts/ and runs all the analyses.

/code/script

It contains functions, and scripts used to retrieve and analyze data.

• code/script/libraries.R: loads the libraries (including the one to retrieve data) and set some parameters.

• code/script/functions_analysis.R: contains main functions used to analyze the data. Documentation on the arguments, and object returned by the functions is reported in the file.

• code/scripts/us_preprocess.R: this is used to obtain U.S data (using the R package covid19census) and preprocess them.

• code/stratified_analysis: it contains code for the stratified analysis model.

• code/secondary_analysis: it contains code for the secondary analysis.

/data

• data_us.RDS: a static copy of the dataframe used for the analysis.

Libraries used and versions

The renc.lock file lists packages and relative version used in the project. Check renv vignette for instructions on how to restore the package environment used for the analyses.

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Sources and data

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 file data/data.Rdata contains a static copy of the data used for the analysis.