finalsize: Calculate final outbreak size or distribution of a multigroup...

In multigroup.vaccine: Analyze Outbreak Models of Multi-Group Populations with Vaccination

Calculate final outbreak size or distribution of a multigroup transmission model for a given basic reproduction number, contact/transmission assumptions, and initial conditions

Description

Calculate final outbreak size or distribution of a multigroup transmission model for a given basic reproduction number, contact/transmission assumptions, and initial conditions

Usage

finalsize(
  popsize,
  R0,
  contactmatrix,
  relsusc,
  reltransm,
  initR,
  initI,
  initV,
  method = "ODE",
  nsims = 1
)

Arguments

popsize	the population size of each group
R0	the basic reproduction number
contactmatrix	matrix of group-to-group contact rates
relsusc	relative susceptibility to infection per contact of each group
reltransm	relative transmissibility per contact of each group
initR	initial number of each group already infected and removed (included in size result)
initI	initial number of each group infectious
initV	initial number of each group vaccinated
method	the method of final size calculation or simulation to use
nsims	the number of simulations to run for stochastic methods

Value

a vector (nsims = 1) or matrix (nsims > 1) with the final number infected from each group (column) in each simulation (row)

Examples

popsize <- c(800, 200)
R0 <- 2
contactmatrix <- contactMatrixPropPref(popsize = popsize, contactrate = c(1, 1),
ingroup = c(0.2, 0.2))
relsusc <- c(1, 1)
reltransm <- c(1, 1)
initR <- c(0, 0)
initI <- c(1, 0)
initV <- 0.2 * popsize
# Default method "ODE" numerical solves ordinary differential equations until infectious count
# is close to 0
finalsize(popsize, R0, contactmatrix, relsusc, reltransm, initR, initI, initV)
finalsize(popsize, R0, contactmatrix, relsusc, reltransm, initR, initI, initV,
method = "analytic")
finalsize(popsize, R0, contactmatrix, relsusc, reltransm, initR, initI, initV,
method = "stochastic", nsims = 10)
# All "escaped" outbreaks set to deterministic final size:
finalsize(popsize, R0, contactmatrix, relsusc, reltransm, initR, initI, initV,
method = "hybrid", nsims = 10)

multigroup.vaccine documentation built on Sept. 19, 2026, 1:06 a.m.