Tag: COVID-19

Members of the R community: be part of the response to COVID-19 (and future epidemic outbreaks)

Dear R users,

We are enthralled to present to you a tool we have been developing with the R epidemics consortium (RECON) thanks to a grant from the R Consortium: the COVID-19 challenge.

It is an online platform whose general goal is to connect members of the R community, R package developers and field agents working on the response to COVID-19 who use R (such as epidemiologists, statisticians or mathematical modellers) to help them fill-in their R related needs. It provides a single place for field agents to give feedback in real time on their analytical needs (such as requesting specific analysis templates, new functions, new method implementation, etc), these requests are then compiled and organized by order of priority (here) for package developers and (hopefully many!) members of the R community to browse and help contribute to.






Many COVID-19 field agents use R to develop their analysis pipelines, but may lack specific knowledge or time to implement some of their needs. That’s why trying to involve the R community in providing them help could turn out to be very important.

For members of the R community it is not only a great opportunity to contribute to the worldwide response to COVID-19 and provide an application of their skills with direct benefit to the community, but it is also a chance to encourage free, open and citizen science through the development of free and open source professional tools who aim at becoming the new standards in epidemic outbreak response.

These packages have already been successfully used in outbreaks such as the Ebola outbreaks in West Africa (2014-2016) and Eastern Democratic Republic of the Congo (2018-2020), and are currently used by various public health institutions and academic modelling groups in the COVID-19 response.

Although this platform has been developed specifically to contribute to the response to COVID-19 we hope to create a dynamic community that will outlast this epidemic, and become a long term methodological contributor.

If you have any question or suggestion, feel free to write to me at [email protected], we welcome all helpful feedback. Also please communicate this to your local R user group, the more you help us get to circulate the word, the most successful the project will be 🙂

Useful links:


Covid-19 interactive map (using R with shiny, leaflet and dplyr)

The departement of Public Health of the Strasbourg University Hospital (GMRC, Prof. Meyer) and the Laboratory of Biostatistics and Medical Informatics of the Strasbourg  Medicine Faculty (Prof. Sauleau), to the extent of their means and expertise, are contributing to the fight against Covid-19 infection. Doctor Fabacher has produced an interactive map for global monitoring of the infection, accessible at :

https://thibautfabacher.shinyapps.io/covid-19/



This map, which complements the Johns Hopkins University tool (Coronavirus COVID-19 Global Cases by Johns Hopkins CSSE), focuses on the evolution of the number of cases per country and for a given period, but in terms of incidence and prevalence. It is updated daily.
The period of interest can be defined by the user and it is possible to choose  :
  • The count of new cases over a period of time or the same count in relation to the population of the country (incidence).
  • The total case count over a period of time or the same count reported to the population (prevalence).

This map is made using R with shiny, leaflet and dplyr packages.

Code available here : https://github.com/DrFabach/Corona/blob/master/shiny.r

Reference
Dong E, Du H, Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis; published online Feb 19. https://doi.org/10.1016/S1473-3099(20)30120-1.