NpiEurope

This research compendium allows you to reproduce the results and figures from Garchitorena et al. (2020).

Live automatic updates

The results and figures are automatically updated on a daily basis using the new data posted on the ECDC website.

Compendium structure

• The script in analysis is used for the Bayesian estimation of the epidemiological parameters. Because these analyses may be very time consuming, it's not advised to run it yourself if you just want to get a feeling of how the code works. By default, this code will run sequentially but can be readily converted to run in parallel thanks to the future package. Here is for example what I use for my local computer:

library(future)
library(parallel)
cl <- makeCluster(4)
plan(cluster, workers = cl)
source('analysis/01-estimate_efficiency_parameters.R', echo=TRUE)

• The output from the script in analysis is saved in MCMC_NpiEurope.

• From the data in MCMC_NpiEurope, the figures of the article are produced with the Rmarkdown files in vignettes. You can see the output of these vignettes by visiting this compendium website.

Do it yourself

To run the code yourself instead of relying of the automatic updates, you will need to first install the functions defined here as well as the package dependencies.

This is done in two steps:

1. Copy the project and open it
2. Install the functions and dependencies

if (!require("usethis")) {
  install.packages("usethis")
}
usethis::create_from_github("Bisaloo/NpiEurope_compendium")

if (!require("devtools")) {
  install.packages("devtools")
}
devtools::install()

You can now run any code from the analysis/ or the vignettes/ folder.