COVID19-world: a shiny application to perform comprehensive country-specific data visualization for SARS-CoV-2 epidemic

Cristian Tebé,Pau Satorra,Joan Valls,Aurelio Tobías

doi:10.1186/s12874-020-01121-9

Abstract

BackgroundData analysis and visualization is an essential tool for exploring and communicating findings in medical research, especially in epidemiological surveillance.ResultsData on COVID-19 diagnosed cases and mortality, from January 1st, 2020, onwards is collected automatically from the European Centre for Disease Prevention and Control (ECDC). We have developed a Shiny application for data visualization and analysis of several indicators to follow the SARS-CoV-2 epidemic using ECDC data. A country-specific tool for basic epidemiological surveillance, in an interactive and user-friendly manner. The available analyses cover time trends and projections, attack rate, population fatality rate, case fatality rate, and basic reproduction number.ConclusionsThe COVID19-World online web application systematically produces daily updated country-specific data visualization and analysis of the SARS-CoV-2 epidemic worldwide. The application may help for a better understanding of the SARS-CoV-2 epidemic worldwide.

Highlights

Data analysis and visualization is an essential tool for exploring and communicating findings in medical research, especially in epidemiological surveillance
The first confirmed case of SARS-CoV-2 in China was reported to the WHO country office in China on December 31st, 2019 [1]
Software The COVID19-World application has been developed in RStudio [6], version 1.2.5033, using the Shiny package, version 1.4.0

Summary

Introduction

Data analysis and visualization is an essential tool for exploring and communicating findings in medical research, especially in epidemiological surveillance [3]. Software The COVID19-World application has been developed in RStudio [6], version 1.2.5033, using the Shiny package, version 1.4.0. The key R packages used in the tool implementation include dplyr, xlsx, and vroom for data management, sjPlot, and EpiEstim for data analysis, shinydashboard, shinyFeedback, shinycssloaders, and kableExtra for application enhancement and plotly for the graphical displays. Tabs, and outputs are available in English, Spanish, and Catalan

Results

Discussion

Conclusion