Single-Facility Disease Transmission Model

Agent-Based Modeling of Disease Transmission in Healthcare

Overview

This is an agent-based model (ABM) built with Repast Simphony 2.11.0 for simulating disease transmission in healthcare facilities.

The model simulates patient flow through a inpatient over approximately 15 years (10-year burn-in + 5-year measurement period), tracking:

  • Patient admissions, lengths of stay, and discharges
  • Disease importation and transmission dynamics
  • Clinical detection and active surveillance testing
  • Decolonization outcomes and isolation effectiveness

Key Features

Model Dynamics

  • Modified SIS Model: Susceptible → Infected/Colonized → Susceptible transmission dynamics
  • Importation: Probability-based disease introduction via new patient admissions
  • Transmission: Beta coefficient-based contact transmission between patients
  • Surveillance: Active surveillance testing with configurable adherence rates
  • Clinical Detection Symptom detection
  • Isolation: Transmission reduction for detected/isolated patients

Output & Analysis

  • CSV outputs for time series analysis in single-run mode
  • CSV outputs that agregate outcomes for batch runs
  • Event logs for admissions, transmissions, detections, etc.
  • Batch running capabilities for parameter sweeps
  • R scripts for verifying model behaviors and sensitivity analyses

Getting Started

Quick Start

  1. Install Requirements: Java 11 + Repast Simphony 2.11.0
  2. Clone Repository: Get the source code
  3. Configure Parameters: Via the Repast Model Runner
  4. Run Simulation: Via the Repast Model Runner
  5. Analyze Results: Use R scripts in analysis/

👉 Get Started →

Documentation

Time Representation

NOTE: Time in this model is continuous floating-point in days: - 1.0 = Start of day 1 - 1.5 = Middle of day 1 - Default total: 5475 ticks = 15 years with or without a 10-year burn-in

Citation

If you use this model in research, please cite:

@software{toth2024,
  title = {Single-Facility Disease Transmission Model},
  author = {Toth, Damon},
  year = {2024},
  url = {https://github.com/EpiForeSITE/single-facility},
  orcid = {0000-0001-7393-4814}
}

Authors & Maintainers

Authors: - Damon Toth (damon.toth@hsc.utah.edu) — ORCID: 0000-0001-7393-4814

Maintainer: - Willy Ray (william.ray@hsc.utah.edu)

Funding

This project was supported by the Centers for Disease Control and Prevention’s Center for Forecasting and Outbreak Analytics under Cooperative Agreement CDC-RFA-FT-23-0069.

Resources