epiworldR (version 0.6.1.0)

ModelSEIRMixing: Susceptible Exposed Infected Removed model (SEIR) with mixing

Description

Susceptible Exposed Infected Removed model (SEIR) with mixing

Usage

ModelSEIRMixing(
  name,
  n,
  prevalence,
  contact_rate,
  transmission_rate,
  incubation_days,
  recovery_rate,
  contact_matrix
)
# S3 method for epiworld_seirmixing
plot(x, main = get_name(x), ...)

Value

• The ModelSEIRMixingfunction returns a model of class epiworld_model.

The plot function returns a plot of the SEIRMixing model of class epiworld_model.

Arguments

name

String. Name of the virus

n

Number of individuals in the population.

prevalence

Double. Initial proportion of individuals with the virus.

contact_rate

Numeric scalar. Average number of contacts per step.

transmission_rate

Numeric scalar between 0 and 1. Probability of transmission.

incubation_days

Numeric scalar. Average number of days in the incubation period.

recovery_rate

Numeric scalar between 0 and 1. Probability of recovery.

contact_matrix

Matrix of contact rates between individuals.

x

Object of class SIRCONN.

main

Title of the plot

...

Currently ignore.

Details

The contact_matrix is a matrix of contact rates between entities. The matrix should be of size n x n, where n is the number of entities. This is a row-stochastic matrix, i.e., the sum of each row should be 1.

The initial_states function allows the user to set the initial state of the model. In particular, the user can specify how many of the non-infected agents have been removed at the beginning of the simulation.

See Also

epiworld-methods

Other Models: ModelDiffNet(), ModelSEIR(), ModelSEIRCONN(), ModelSEIRD(), ModelSEIRDCONN(), ModelSIR(), ModelSIRCONN(), ModelSIRD(), ModelSIRDCONN(), ModelSIRLogit(), ModelSIRMixing(), ModelSIS(), ModelSISD(), ModelSURV(), epiworld-data

Examples

# Start off creating three entities.
# Individuals will be distribured randomly between the three.
e1 <- entity("Population 1", 3e3, as_proportion = FALSE)
e2 <- entity("Population 2", 3e3, as_proportion = FALSE)
e3 <- entity("Population 3", 3e3, as_proportion = FALSE)

# Row-stochastic matrix (rowsums 1)
cmatrix <- c(
  c(0.9, 0.05, 0.05),
  c(0.1, 0.8, 0.1),
  c(0.1, 0.2, 0.7)
) |> matrix(byrow = TRUE, nrow = 3)

N <- 9e3

flu_model <- ModelSEIRMixing(
  name              = "Flu",
  n                 = N,
  prevalence        = 1 / N,
  contact_rate      = 20,
  transmission_rate = 0.1,
  recovery_rate     = 1 / 7,
  incubation_days   = 7,
  contact_matrix    = cmatrix
)

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

set.seed(331)
run(flu_model, ndays = 100)
summary(flu_model)
plot_incidence(flu_model)