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EpiModel Web

Source: R/shiny.R
epiweb.Rd

Launches interactive Shiny applications for exploring deterministic compartmental models (DCMs) and stochastic individual contact models (ICMs) of infectious disease transmission.

Usage

epiweb(class, ...)

Arguments

class

Model class, with options of "dcm" and "icm".

...

Additional arguments passed to shiny::runApp, such as port, host, or launch.browser.

Details

epiweb launches a web-based graphical interface for configuring, running, and analyzing epidemic models built on EpiModel. Each application provides interactive controls for model parameters, real-time (or on-demand) visualization with plotly, narrative model summaries, and downloadable data tables. Both applications include a Guide tab with a comprehensive user manual covering the underlying theory, parameter definitions, and instructions for interpreting output.

DCM Application (class = "dcm")

The DCM app solves systems of ordinary differential equations for one-group SI, SIR, and SIS models. Models run instantly and the interface is fully reactive (no run button). Features include:

  • Scenario presets: Flu-like (SIR), STI-like (SIS), and Measles-like (SIR) configurations that set all parameters to epidemiologically plausible values.

  • Interventions: An optional mid-epidemic intervention that reduces the transmission probability by a user-specified efficacy, shown as a vertical dashed line on the plot.

  • Sensitivity analysis: Vary any epidemic parameter across a range of values to compare trajectories side by side with a blue-to-red color ramp.

  • Vital dynamics: Optional births and deaths to model endemic equilibria over longer time horizons.

  • Summary tab: Displays the basic reproduction number (R0), peak timing, cumulative infections, attack rate, and contextual interpretation.

  • Data tab: Searchable table of model output with CSV download.

ICM Application (class = "icm")

The ICM app runs agent-based stochastic microsimulations for one-group SI, SIR, and SIS models. Because ICMs are computationally more expensive, a Run Model button controls when simulations execute. Features include:

  • Stochastic visualization: Multiple simulations are summarized with mean trajectory lines and interquartile range (IQR) ribbons showing the middle 50\ individual trajectories.

  • Scenario presets: The same Flu-like, STI-like, and Measles-like configurations as the DCM app, adapted for smaller populations suitable for agent-based simulation.

  • Interventions: Same intervention system as DCM, natively supported by param.icm.

  • Vital dynamics: Optional births and deaths, as in DCM.

  • Summary tab: Displays R0, epidemic timeline from the mean trajectory, and a stochastic variation section showing the range and standard deviation of peak infections and final prevalence across simulations.

  • Data tab: View simulation output as means, standard deviations, or individual simulation values, with CSV download.

Required Packages

Both applications require the shiny, bslib, DT, and plotly packages. Install any missing packages with install.packages(c("shiny", "bslib", "DT", "plotly")).

See also

dcm and param.dcm for the DCM modeling API; icm and param.icm for the ICM modeling API.

Examples

if (FALSE) { # \dontrun{
## Deterministic compartmental models
epiweb(class = "dcm")

## Stochastic individual contact models
epiweb(class = "icm")
} # }