measles

Overview

The measles package is a specialized spinoff from epiworldR, focusing exclusively on measles epidemiological models. This package provides fast, agent-based models (ABMs) for studying measles transmission dynamics, vaccination strategies, and intervention policies.

Built on the powerful epiworld C++ library, these models leverage the speed and flexibility of epiworldR while providing specialized functionality for measles outbreak modeling.

Features

• Fast simulation: Leverages the high-performance C++ backend from epiworld
• Specialized measles models: Three distinct models tailored for different scenarios
• Flexible interventions: Support for vaccination, quarantine, isolation, and contact tracing
• Population mixing: Models can account for different population groups with varying contact patterns
• Risk-based strategies: Advanced models support risk-stratified quarantine policies

Models Included

The package includes three measles-specific models:

1. ModelMeaslesSchool: A SEIHR (Susceptible-Exposed-Infectious-Hospitalized-Recovered) model designed for school settings with isolation and quarantine policies.

2. ModelMeaslesMixing: A measles model with population mixing between different groups, including vaccination, quarantine, isolation, and contact tracing mechanisms.

3. ModelMeaslesMixingRiskQuarantine: An advanced mixing model with risk-based quarantine strategies that assign different quarantine durations based on exposure risk levels (high, medium, low).

Installation

You can install the measles package from GitHub:

# install.packages("devtools")
devtools::install_github("UofUEpiBio/measles")

Note: This package requires epiworldR as a dependency.

Quick Example

Here’s a simple example using the ModelMeaslesSchool:

library(measles)

# Create a measles model for a school with 500 students
model_school <- ModelMeaslesSchool(
  n = 500,
  prevalence = 1,
  prop_vaccinated = 0.70,
  contact_rate = 15,
  transmission_rate = 0.9
)

# Run the simulation
run(model_school, ndays = 100, seed = 1912)

# View results
summary(model_school)
plot(model_school)

Example with Population Mixing

The mixing models allow you to simulate measles spread across different population groups:

library(measles)

# Define three populations
e1 <- entity("Population 1", 3000, as_proportion = FALSE)
e2 <- entity("Population 2", 3000, as_proportion = FALSE)
e3 <- entity("Population 3", 3000, as_proportion = FALSE)

# Define contact matrix (row-stochastic: rows sum to 1)
contact_matrix <- matrix(c(
  0.9, 0.05, 0.05,
  0.1, 0.8,  0.1,
  0.1, 0.2,  0.7
), byrow = TRUE, nrow = 3)

# Create the model
measles_model <- ModelMeaslesMixing(
  n = 9000,
  prevalence = 1 / 9000,
  contact_rate = 15,
  transmission_rate = 0.9,
  vax_efficacy = 0.97,
  prop_vaccinated = 0.95,
  contact_matrix = contact_matrix,
  quarantine_period = 14,
  isolation_period = 10
)

# Add entities and run
measles_model |>
  add_entity(e1) |>
  add_entity(e2) |>
  add_entity(e3)

run(measles_model, ndays = 100, seed = 331)
summary(measles_model)

Relationship to epiworldR

This package is a spinoff from epiworldR, which provides a comprehensive framework for agent-based epidemiological models. While epiworldR includes many different disease models (SIR, SEIR, SIS, etc.), the measles package focuses specifically on measles-related models with specialized features for:

• Measles-specific disease progression (incubation, prodromal, and rash periods)
• School-based outbreak scenarios
• Vaccination coverage and efficacy
• Quarantine and isolation policies
• Contact tracing strategies
• Risk-stratified interventions

For general-purpose epidemiological modeling or other disease types, please see the epiworldR package.

Citation

If you use the measles package in your research, please cite both this package and epiworldR:

citation("measles")
citation("epiworldR")

Authors

This package was developed as part of a collaboration between the University of Utah (ForeSITE center grant) and the Utah Department of Health and Human Services in response to the 2025 US Measles outbreak.

License

MIT License - see LICENSE file for details.

Contributing

Contributions are welcome! Please see the epiworldR development guidelines for information on how to contribute.