RShiny App: Analysis of subnational COVID-19 outbreak risk in the EU/EEA in the vaccine era

To run the Shiny app locally, install the shiny package, set the working directory to this repository, and run shiny::runApp("Scripts_RShiny/"). You will need to have the packages listed in the first lines of ui.R (shiny, leaflet, dplyr, sf, ggplot2, and surveillance) installed on your computer.

The file "Rshiny App user guide" contains the user guide of the Shiny app.

This repository contains four R scripts and three data files (all located in the folder Scripts_RShiny).

• Scripts_RShiny/output_model_FR.RDS, Scripts_RShiny/output_model_CZ.RDS, and Scripts_RShiny/output_model_IT_total.RDS are output files generated by the backend scripts. They contain simulation sets, predictors values, maps, and model output generated in each country.
• Scripts_RShiny/ui.R is a script defining the user interface of the shiny app. It describes how the buttons, options, and plots integrated in the Shiny app are arranged and labeled.
• Scripts_RShiny/server.R defines the server logic of the shiny app, i.e it links changes in the user interface to the functions implemented in function_shiny.R and function_server.R.
• Scripts_RShiny/function_shiny.R contains the different functions used to generate the figures integrated in the Shiny app.
• Scripts_RShiny/function_server.R: contains a function wrapping plot_time_series() depending on the selected inputs.

Authors

• Alexis Robert: [email protected]
• Lloyd Chapman: [email protected]