Last updated: 2026-04-15
EpiLinx is an R Shiny application for exploring hospital contact patterns through interactive visualizations. At its core, EpiLinx implements an algorithm that identifies overlapping hospital stays between patients across departments and institutions.
By quantifying these overlaps, EpiLinx enables users to investigate potential pathways of contact and transmission. The app provides a variety of interactive plots and tables that support exploration at multiple levels — from individual patients to departments and entire hospitals.
EpiLinx is designed to support epidemiological analysis by making complex temporal overlap structures accessible and interpretable through an intuitive interface.
For more details, see the documentation and examples included in this repository.
The EpiLinx package requires installation of the statistical programming software R. Installers for Linux, macOS and Windows can be downloaded from The Comprehensive R Archive Network at CRAN
You can install EpiLinx from R by:
install.packages(
"EpiLinx",
repos = c("https://ku-awdc.r-universe.dev/", "https://cran.rstudio.com/")
)EpiLinx is an interactive Shiny application for exploring overlapping
hospital stays.
In most cases, you simply launch the app and explore the data through
the user interface.
library(EpiLinx)
run_app()EpiLinx has been routinely used in the Danish outbreak surveillance for over six years, supporting weekly analyses of hospital contact patterns.
The tool has been applied in real-world epidemiological investigations and has contributed to multiple studies on transmission dynamics and healthcare-associated contacts. EpiLinx has been used in the following studies:
- Characterization of carbapenemase-producing Acinetobacter baumannii isolates from Danish patients 2014-2021: detection of a new international clone – IC11
- Contaminated dicloxacillin capsules as the source of an NDM-5/OXA-48-producing Enterobacter hormaechei ST79 outbreak, Denmark and Iceland, 2022 and 2023
- Surveillance of OXA-244-producing Escherichia coli and epidemiologic investigation of these cases, Denmark, May 2016 - July 2019
- Investigation of possible transmission of carbapenemase-producing Klebsiella pneumonia complex members in Denmark using core genome MLST and national patient registry data
- Real-time FT-IR typing Klebsiella pneumoniae: a flexible and rapid approach for outbreak detection and infection control