Estimate reproduction number from contact information and immunity profile

This takes a contact survey to derive a contact matrix and rescales contacts to represent contacts with susceptibles. This is then combined with information on the basic reproduction number R0 to calculate the effective or net reproduction number.

Usage

adjust_immunity(mixing_matrix, immunity, vector = FALSE)

Arguments

mixing_matrix: A mixing matrix, as returned by socialmixr::contact_matrix
immunity: immunity profile; this should be given as a vector of the same length as the number of rows/columns of the mixing matrix; each element of the vector should contain a value <1 representing the proportion of the population immune in the corresponding age group; any element set to "herd" will be set to 1-1/R0
vector: if TRUE, will return the eigenvector corresponding to the dominant eigenvector instead of adjusted immunity; this corresponds to the expected stable age distribution of infections in case of an outbreak

Value

a list contain vectors of adjusted immunities

Author

Sebastian Funk

Examples

library("socialmixr")
#> 
#> Attaching package: ‘socialmixr’
#> The following object is masked from ‘package:utils’:
#> 
#>     cite
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
adjust_immunity(mixing$matrix, immunity = c(0, 0.5, 0.8))
#> [1] 0.7069723