Calculates the age distribution of an epidemic — epidemic_age

calculates the age distribution in an epidemic setting using the iterative method of: J Wallinga, P Teunis, M Kretschmar (2006) Using Data on Social Contacts to Estimate Age-specific Transmission Parameters for Respiratory-spread Infectious Agents. Am J Epidemiol 164(10), 945-946.

Usage

epidemic_age_dist(
  mixing_matrix,
  r_0,
  immunity = 0,
  final_size_start = 0.01,
  tol = 1e-05
)

Arguments

mixing_matrix: A mixing matrix or set of mixing matrices, as returned by socialmixr::contact_matrix
r_0: basic reproduction number
immunity: proportion immune before the epidemic
final_size_start: starting value for inidence
tol: tolerance for stopping the iteration

Value

A matrix of the final size(s) (proportion of susceptibles infected) in each age group (one row per matrix contained in mixing)

Examples

library("socialmixr")
mixing <- contact_matrix(survey = polymod, age.limits = c(0, 5, 10))
#> Using POLYMOD social contact data. To cite this in a publication, use the 'cite' function
#> Removing participants without age information. To change this behaviour, set the 'missing.participant.age' option
#> Removing participants that have contacts without age information. To change this behaviour, set the 'missing.contact.age' option
epidemic_age_dist(mixing$matrix, r_0 = 5, immunity = 0.50)
#>        [0,5)    [5,10)      10+
#> [1,] 0.18991 0.4972204 0.959609