Analyze Outbreak Models of Multi-Group Populations with Vaccination

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Documentation for package ‘multigroup.vaccine’ version 0.1.1

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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