https://github.com/bisaloo/npieurope_compendium

https://github.com/bisaloo/npieurope_compendium

Last synced: 29 days ago
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• Host: GitHub
• URL: https://github.com/bisaloo/npieurope_compendium
• Owner: Bisaloo
• Created: 2020-12-02T12:15:02.000Z (about 4 years ago)
• Default Branch: main
• Last Pushed: 2021-03-29T13:40:53.000Z (almost 4 years ago)
• Last Synced: 2024-10-24T16:18:29.598Z (3 months ago)
• Language: R
• Homepage: https://bisaloo.github.io/NpiEurope_compendium
• Size: 1.17 MB
• Stars: 2
• Watchers: 4
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

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README

        
# NpiEurope

This [research compendium](https://doi.org/10.1080/00031305.2017.1375986) allows

you to reproduce the results and figures from 

[Garchitorena *et al.* (2020)](https://doi.org/10.1101/2020.08.17.20174821).

## 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](https://cran.r-project.org/package=future) package. Here is for example

what I use for my local computer:

```r

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](https://bisaloo.github.io/NpiEurope_compendium).

## 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

1. Install the functions and dependencies

```r

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.