R: Analyze Outbreak Models of Multi-Group Populations with Vaccination

# Analyze Outbreak Models of Multi-Group Populations with Vaccination

## Documentation for package ‘multigroup.vaccine’ version 0.1.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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