kashenfelter / covid19_cases_from_deaths

Shiny app to infer caes from new deaths of COVID-19

Using the shiny app

All content below relates to the app/ folder.

What this does

Infer the number of circulating COVID-19 cases from newly reported deaths. This is expected to be useful in places where surveillance has not picked up cases yet, and new deaths are the only indication that there are more circulating cases.

How to use it

Packages needed

The following instructions will install the packages needed if they are not present on your system:

if (!require(pacman)) {
  install.packages("pacman")
  library(pacman)
}
p_load("shiny")
p_load("ggplot2")
p_load("magrittr")
p_load("incidence")
p_load("projections")
p_load("distcrete")
p_load("DT")
p_load_gh("reconhub/reportfactory")

Note that you only need to do this once (or not at all, if all these packages are already on your system).

Starting the app

To start the app, open R inside this folder and type shiny::runApp("death_to_case.R"). If using Rstudio, make sure you view the app within a decent web browser by clicking on "Open in Browser".

Disclaimer

This is work in progress, which has not been peer-reviewed yet. Do not use without consulting me before.