idcup

Agent-based measles outbreak simulations across major U.S. cities, built on epiworldR and the measles R package. Scenarios are parameterized Quarto documents that can be rendered per city using census-derived age structure and MMR vaccination coverage.

Cities covered

Los Angeles, San Francisco, New York City, Boston, Houston, Dallas, Philadelphia, Atlanta, Seattle, Miami, Kansas City.

Repository layout

data/
  census_age.csv       Age-structured population counts by city (generated)
  census_age.R         Script to pull county-level census data via multigroup.vaccine
  population.csv       Total city populations (source: census.gov)
  mmr.csv              MMR vaccination estimates by city (source: CDC MMWR 2023-24)
scenarios/
  template.qmd         Parameterized Quarto scenario document
  data/                City-specific data symlinked/copied for rendering
Makefile               Targets for data generation and package updates

Getting started

Prerequisites

Install the required R packages from GitHub:

# Core simulation engine
remotes::install_github("UofUEpiBio/epiworldR")

# Measles model and helpers
remotes::install_github("UofUEpiBio/measles")

# Census data utilities (used by census_age.R)
remotes::install_github("EpiForeSITE/multigroup.vaccine")

Or use the Makefile targets:

make update-epiworldr
make update-measles

Regenerate census age data

make data/census_age.csv

This calls data/census_age.R, which queries 2024 county-level census data for each city and writes data/census_age.csv.

Run a scenario

Render the template for a specific city:

quarto render scenarios/template.qmd -P city:"Miami"

Data sources

File	Source
population.csv	U.S. Census Bureau
census_age.csv	U.S. Census Bureau (2024, county-level, via multigroup.vaccine)
mmr.csv	CDC MMWR 2023–24 kindergarten vaccination coverage

Relevant age groups:

• 0to4
• 5to9
• 10to14
• 15to19
• 20to24
• 25to29
• 30to34
• 35to39
• 40to44
• 45to49
• 50to54
• 55to59
• 60to64
• 65to69
• 70to74
• 75to79
• 80to84
• 85plus

Model overview

Each scenario runs an age-structured ModelMeaslesMixing simulation with:

• Age-stratified population from census data
• Proportional contact mixing matrix
• MMR vaccine efficacy of 97%
• Configurable vaccination coverage, hospitalization probability, quarantine/isolation parameters, and contact tracing
• 50 stochastic replicate runs over 100 simulated days