Get or set the contact matrix of a mixing model

Usage

get_contact_matrix(model)

set_contact_matrix(model, contact_matrix, as_backup = TRUE)

Arguments

model: An object of class epiworld_model that supports contact matrices.
contact_matrix: A numeric matrix with the contact matrix to be set for the model. The matrix should be square and have the same number of rows as the number of entities in the model.
as_backup: A logical value indicating whether to save the new contact matrix as a backup in the model. If TRUE (default), the new contact matrix will be saved as a backup in the model, automatically restoring its value if it changes during the simulation.

Value

The get_contact_matrix() function returns the contact matrix of the model as a numeric matrix.

The set_contact_matrix() function sets the contact matrix of the model to the provided matrix and returns the modified model invisibly. The function is called for its side effects and returns the modified model invisibly.

Examples

cmatrix <- (c(
  c(0.9, 0.05, 0.05),
  c(0.1, 0.8, 0.1),
  c(0.1, 0.2, 0.7)
) * 20) |> matrix(byrow = TRUE, nrow = 3)


N <- 9e3

flu_model <- ModelSIRMixing(
  name              = "Flu",
  n                 = N,
  prevalence        = 1 / N,
  transmission_rate = 0.1,
  recovery_rate     = 1 / 7,
  contact_matrix    = cmatrix
)

get_contact_matrix(flu_model)
#>      [,1] [,2] [,3]
#> [1,]   18    1    1
#> [2,]    2   16    2
#> [3,]    2    4   14
#' # Modifying the contact matrix
new_cmatrix <- (c(
  c(0.8, 0.1, 0.1),
  c(0.1, 0.7, 0.2),
  c(0.1, 0.2, 0.7)
) * 20) |> matrix(byrow = TRUE, nrow = 3)
set_contact_matrix(flu_model, new_cmatrix)
get_contact_matrix(flu_model)
#>      [,1] [,2] [,3]
#> [1,]   16    2    2
#> [2,]    2   14    4
#> [3,]    2    4   14