Package index • multigroup.vaccine

All functions

aggregateByAgeGroups(): Aggregate population counts into age groups
contactMatrixAgeSchool(): Calculate a contact matrix for age groups and schools
contactMatrixPolymod(): Calculate a contact matrix for age groups based on Polymod contact survey data
contactMatrixPropPref(): Calculate group contact matrix with proportional mixing and preferential mixing within group
finalsize(): Calculate final outbreak size or distribution of a multigroup transmission model for a given basic reproduction number, contact/transmission assumptions, and initial conditions
getCensusData(): Get Census Population Data by Age and County
getCensusDataPath(): Get path to example census data file
getCityData(): Get City Population Data by Age
getFinalSizeAnalytic(): Calculate final size of outbreak: the total number of infections in each group, by solving the analytic final size equation
getFinalSizeDist(): Estimate the distribution of final outbreak sizes by group using stochastic simulations of multi-group model
getFinalSizeDistEscape(): Estimate the distribution of final outbreak sizes by group using a hybrid model: stochastic simulations for smaller-sized outbreaks and deterministic ordinary differential equation model for "escaped" outbreaks
getFinalSizeODE(): Calculate outbreak final size, the total number of infections in each group, by numerically solving the multi-group ordinary differential equation
getSizeAtTime(): Calculate outbreak size at a given time
getStateFIPS(): Get state FIPS code by state name
listCounties(): List available counties for a state
odeSIR(): Ordinary differential equation function for multi-group susceptible-infectious-removed (SIR) model used as "func" argument passed to the ode() function from deSolve package
run_my_app(): Runs the shiny app
transmissionRates(): Calculate transmission rate matrix for multi-group model with specified R0
vaxrepnum(): Calculate reproduction number for a multigroup model with a given state of vaccination and immunity