A 'Shiny' App to Simulate the Dynamics of Epidemic and Endemic Diseases Spread

The 'EpiSimR' package provides an interactive 'shiny' app based on deterministic compartmental mathematical modeling for simulating and visualizing the dynamics of epidemic and endemic disease spread. It allows users to explore various intervention strategies, including vaccination and isolation, by adjusting key epidemiological parameters. The methodology follows the approach described by Brauer (2008) . Thanks to 'shiny' package.

EpiSimR

Overview

EpiSimR is an R Shiny application designed for simulating the dynamics of epidemic and endemic disease spread. It utilizes deterministic compartmental mathematical models to provide interactive visualizations and insights into disease transmission and control strategies.

Description

EpiSimR offers an interactive platform for modeling the spread of infectious diseases. Users can select different epidemiological models, including:

• SIR (Susceptible-Infectious-Recovered)
• SEIR (Susceptible-Exposed-Infectious-Recovered)

The app allows users to configure various parameters, such as:

• Inclusion or exclusion of permanent immunity
• Consideration of demographic changes
• Implementation of vaccination and isolation strategies

Users can adjust key epidemiological parameters, including:

• Basic reproduction number (R₀)
• Birth and mortality rates
• Infectious and latent periods
• Immunity duration
• Vaccination coverage
• Isolation rate

By modifying these parameters, users can simulate and visualize disease progression under different conditions and intervention strategies.

Installation

To install the package, use:

# Install from GitHub
devtools::install_github("NassimAyad87/EpiSimR", dependencies = TRUE)

Usage

Launch the Shiny application using:

library(EpiSimR)
run_app()

Features

Model Selection & Customization

• Choose between SIR and SEIR models.
• Include or exclude permanent immunity.
• Consider demographic changes.
• Customize vaccination and isolation strategies.

Parameter Adjustments

• Basic reproduction number (R₀)
• Birth and mortality rates
• Infectious period
• Latent period (for SEIR model)
• Immunity duration
• Vaccination coverage
• Isolation rate

Simulation & Interactive Visualization

• Real-time simulation of epidemic and endemic dynamics.
• Interactive graphical representation of disease spread over time.
• Visual assessment of public health intervention impacts (e.g., vaccination, isolation).

User-Friendly Interface

• Built with Shiny for an intuitive and interactive experience.
• Dynamic updates based on user inputs.

Application Purpose

• Serves as an educational and analytical tool for understanding epidemiological modeling.
• Assists in evaluating the effectiveness of public health interventions.

License

This package is licensed under the GPL-3 License.