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 row-stochastic matrix representing contact rates between population groups. The matrix should be square with dimensions matching the number of entities (population groups) in the model, and each row should sum to 1.

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

The contact matrix is a row-stochastic matrix where entry [i, j] represents the probability that an individual in group i will make contact with someone in group j, given that they make a contact. Each row must sum to 1.

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)

N <- 3000

# Create a measles mixing model
model <- ModelMeaslesMixing(
  n                        = N,
  prevalence               = 1 / N,
  contact_rate             = 15,
  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_prior = 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,]    1    0    0
#> [2,]    0    1    0
#> [3,]    0    0    1

# Create a new random row-stochastic matrix
new_matrix <- matrix(
  c(0.8, 0.1, 0.1,
    0.1, 0.7, 0.2,
    0.15, 0.15, 0.7),
  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,] 0.80 0.10  0.1
#> [2,] 0.10 0.70  0.2
#> [3,] 0.15 0.15  0.7