Analyze Outbreak Models of Multi-Group Populations with Vaccination
Aggregate population counts into age groups
Calculate a contact matrix for age groups and schools
Calculate a contact matrix for age groups based on Polymod contact sur...
Calculate group contact matrix with proportional mixing and preferenti...
Disaggregate ACS 5-year age groups into single-year ages
Calculate final outbreak size or distribution of a multigroup transmis...
Get Census Population Data by Age and County
Get path to example census data file
Get City Population Data by Age
Calculate final size of outbreak: the total number of infections in ea...
Estimate the distribution of final outbreak sizes by group using stoch...
Estimate the distribution of final outbreak sizes by group using a hyb...
Calculate outbreak final size, the total number of infections in each ...
Calculate outbreak size at a given time
Get state FIPS code by state name
List available counties for a state
Ordinary differential equation function for multi-group susceptible-in...
Process census data with sex disaggregation
Process census data without sex disaggregation
Runs the shiny app
Calculate transmission rate matrix for multi-group model with specifie...
Calculate reproduction number for a multigroup model with a given stat...
Model infectious disease dynamics in populations with multiple subgroups having different vaccination rates, transmission characteristics, and contact patterns. Calculate final and intermediate outbreak sizes, form age-structured contact models with automatic fetching of U.S. census data, and explore vaccination scenarios with an interactive 'shiny' dashboard for a model with two subgroups, as described in Nguyen et al. (2024) <doi:10.1016/j.jval.2024.03.039> and Duong et al. (2026) <doi:10.1093/ofid/ofaf695.217>.