process_I_multivariant: Process incidence input for multivariant analyses with...

In annecori/EpiEstim: Estimate Time Varying Reproduction Numbers from Epidemic Curves

Process incidence input for multivariant analyses with estimate_advantage

Description

Process incidence input for multivariant analyses with estimate_advantage

Usage

process_I_multivariant(incid, incid_imported = NULL)

Arguments

incid

a multidimensional array containing values of the incidence for each time step (1st dimension), location (2nd dimension) and pathogen/strain/variant (3rd dimension)

incid_imported

an optional multidimensional array containing values of the incidence of imported cases for each time step (1st dimension), location (2nd dimension) and pathogen/strain/variant (3rd dimension). 'incid - incid_imported' is therefore the incidence of locally infected cases. If 'incid_imported' is NULL this means there are no known imported cases and all cases other than on those from the first time step will be considered locally infected.

Value

a list with two elements. 1) 'local' a multidimensional array containing values of the incidence of locally infected cases for each time step (1st dimension), location (2nd dimension) and pathogen/strain/variant (3rd dimension) 2) 'imported' a multidimensional array containing values of the incidence of imported cases for each time step (1st dimension), location (2nd dimension) and pathogen/strain/variant (3rd dimension)

Examples

n_v <- 3 # 3 variants
n_loc <- 1 # 1 location
T <- 100 # 100 time steps
# constant incidence 10 per day everywhere
incid <- array(10, dim = c(T, n_loc, n_v))
process_I_multivariant(incid)

annecori/EpiEstim documentation built on Oct. 14, 2023, 1:54 a.m.