README.md

In MESuRS-Lab/mwss: Stochastic simulations of infectious disease spread in healthcare systems structured as a networked metapopulation

--- Package under development ---

mwss: an R package for stochastic simulation of infectious diseases spreading in healthcare systems structured as networked metapopulations

Hammami Pachka1,2,3,, Oodally Ajmal1,2,3,, Reilhac Astrid4, Guérineau de Lamérie Guillaume4, Widgren Stefan 5, Temime Laura3,6,¤ and Opatowski Lulla1,2,¤

1 Anti-infective evasion and pharmacoepidemiology team, Université Paris-Saclay, UVSQ, Inserm, CESP, Montigny-Le-Bretonneux, France

2 Epidemiology and Modelling of Antibiotic Evasion (EMAE), Institut Pasteur, Paris, France

3 Laboratoire de Modélisation, épidémiologie et surveillance des risques sanitaires (MESuRS), Conservatoire national des arts et métiers, Paris, France

4 Département d'information médicale, Centre hospitalier Guillaume Régnier, Rennes, France

5 Department of Disease Control and Epidemiology, National Veterinary Institute, Uppsala, Sweden

6 PACRI unit, Institut Pasteur, Conservatoire national des arts et métiers, Paris, France 7MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, United Kingdom

*These authors contributed equally

¤These authors contributed equally

Corresponding author: Hammami Pachka ([e-mail])

Installation

The package can be install using 'devtools' library:

library(devtools)
install_github("MESuRS-Lab/mwss")

The companion RShiny application providing user-friendly interface to run simulations can be loaded directly from the GitHub repository (https://github.com/MESuRS-Lab/mwss-App) using 'shiny' library:

library(shiny) # use version >= 1.7.1
runGitHub("MESuRS-Lab/mwss-App")

Main contents

This repository contains the source code for the "mwss" package developed using R-programming language. This package allows the user to run multi-ward stochastic simulations to simulate virus transmission in the hospital setting.

mwss
├── R
├── data
├── man
├── DESCRIPTION
├── NAMESPACE
├── mwss.Rproj

• R This folder contains all the package functions

• Data This folder contains the toydataset to run the examples documented for each exported function.

Further actions

• sensitivity analysis
• publications

MESuRS-Lab/mwss documentation built on Sept. 12, 2023, 12:08 a.m.