--- Application under development ---
mwss-App: an R-Shiny application to run stochastic simulation of infectious diseases spreading in healthcare systems structured as networked metapopulations
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 ([email protected])
Open your R console or RStudio and paste the commands provided below. mwss-App will automatically install all required dependencies (R packages).
library("shiny")
runGitHub("MESuRS-Lab/mwss-App")
The main package used is mwss available in our GitHub page: https://github.com/MESuRS-Lab/mwss
Required Shiny version >= 1.7.1
This version of mwss-App was developed on R version 4.1.3 (2022-03-10) with Windows 10 x64 (build 18363) using the following version of dependencies:
mwss-App
├── shiny_1.7.1
├── shinyalert_3.0.0
├── shinydashboard_0.7.2
├── shinyhelper_0.3.2
├── shinyjs_2.1.0
├── shinyTime_1.0.1
├── shinyWidgets_0.7.0
├── DT_0.23
├── data.table_1.14.2
├── SimInf_9.0.0
├── statnet_2019.6
├── igraph_1.3.1
├── network_1.17.2
├── plotly_4.10.0
├── magrittr_2.0.3
├── dplyr_1.0.9
├── knitr_1.39
├── devtools_2.4.3
├── ggplot2_3.3.6
The package mwss developed simultaneously should always be up to date with the online version.
library(remotes)
install_github("MESuRS-Lab/mwss")
This repository contains the source code for the "mwss-App" RShiny application developed using R-programming language. The RShiny application provides a comprehensive, user-friendly interface to run complex stochastic simulations for the nosocomial spread of Covid-19 in multi-service healthcare systems.
mwss-App
├── body
├── data
├── functions
├── header
├── helpfiles
├── www
├── report.Rmd
├── app.R
├── global.R
├── server.R
├── ui.R
-
body
This folder contains the main ui files shaping the different panels. -
data
This folder contains the toydataset and parameters for different Covid-19 variants. -
functions
This folder contains the modules. -
header
This folder contains the ui file designing the header. -
helpfiles
This folder contains the markdown content of help notes. -
www
This folder contains the images displayed in the application. -
** report.Rmd **
This RMarkdown file contains the structure of the report that can be downloaded after runing simulations. -
R files
-
app.R
-
global.R
-
server.R
-
ui.R Those files are baseline files for Rshiny application (read more on: https://shiny.rstudio.com/articles/scoping.html)
- complete report content
- define parameters for two variants (e.g. alpha and omicron) & fill References tabs
- test by modelers (Lulla, Ajmal, Laura) -> test by clinicians (Hackathon)
- upgrade
- publication