Get and Set Contact Matrix — contact

These functions allow getting and setting the contact matrix for measles mixing models. The contact matrix specifies the mixing patterns between different population groups.

Usage

get_contact_matrix(model)

# Default S3 method
get_contact_matrix(model)

# S3 method for class 'epiworld_measlesmixing'
get_contact_matrix(model)

# S3 method for class 'epiworld_measlesmixingriskquarantine'
get_contact_matrix(model)

set_contact_matrix(model, value)

# Default S3 method
set_contact_matrix(model, value)

# S3 method for class 'epiworld_measlesmixing'
set_contact_matrix(model, value)

# S3 method for class 'epiworld_measlesmixingriskquarantine'
set_contact_matrix(model, value)

Arguments

model: An epiworld model object of class epiworld_measlesmixing or epiworld_measlesmixingriskquarantine.
value: A numeric square matrix representing contact rates between population groups. The matrix should have one row and one column per entity in the model.

Value

get_contact_matrix() returns a numeric matrix representing the contact rates between population groups.
set_contact_matrix() returns the model object invisibly (called for its side effects).

Details

Entry [i, j] of the contact matrix represents the expected number of contacts that an individual in group i has with individuals in group j during a time step.

These functions are currently only available for:

Other mixing models in epiworld will have these methods available in the near future.

Examples

# Create entities for three population groups
e1 <- entity("Population 1", 1000, as_proportion = FALSE)
e2 <- entity("Population 2", 1000, as_proportion = FALSE)
e3 <- entity("Population 3", 1000, as_proportion = FALSE)

# Create an identity contact matrix (no mixing between groups)
cmatrix <- diag(3) * 15

N <- 3000

# Create a measles mixing model
model <- ModelMeaslesMixing(
  n                        = N,
  prevalence               = 1 / N,
  transmission_rate        = 0.9,
  vax_efficacy             = 0.97,
  vax_reduction_recovery_rate = 0.8,
  incubation_period        = 10,
  prodromal_period         = 3,
  rash_period              = 7,
  contact_matrix           = cmatrix,
  hospitalization_rate     = 0.1,
  hospitalization_period   = 10,
  days_undetected          = 2,
  quarantine_period        = 14,
  quarantine_willingness   = 0.9,
  isolation_willingness    = 0.8,
  isolation_period         = 10,
  prop_vaccinated          = 0.95,
  contact_tracing_success_rate = 0.8,
  contact_tracing_days_window = 4
)

# Add entities to the model
model |>
  add_entity(e1) |>
  add_entity(e2) |>
  add_entity(e3)

# Get the contact matrix (note: requires running the model first)
set.seed(123)
run(model, ndays = 10)
#> _________________________________________________________________________
#> |||||||Running the model...
#> |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
#> |||||||
original_matrix <- get_contact_matrix(model)
print(original_matrix)
#>      [,1] [,2] [,3]
#> [1,]   15    0    0
#> [2,]    0   15    0
#> [3,]    0    0   15

# Create a new contact matrix
new_matrix <- matrix(
  c(12, 1.5, 1.5,
    2, 11, 2,
    2.25, 2.25, 10.5),
  nrow = 3, byrow = TRUE
)

# Set the new contact matrix
set_contact_matrix(model, new_matrix)

# Verify the change
updated_matrix <- get_contact_matrix(model)
print(updated_matrix)
#>       [,1]  [,2] [,3]
#> [1,] 12.00  1.50  1.5
#> [2,]  2.00 11.00  2.0
#> [3,]  2.25  2.25 10.5