R/ModelSEIR.R

In epiworldR: Fast Agent-Based Epi Models

#' Susceptible Exposed Infected Recovered model (SEIR)
#'
#' @param name String. Name of the virus.
#' @param prevalence Double. Initial proportion of individuals with the virus.
#' @param transmission_rate Numeric scalar between 0 and 1. Virus's rate of
#' infection.
#' @param incubation_days Numeric scalar greater than 0. Average number of
#' incubation days.
#' @param recovery_rate Numeric scalar between 0 and 1. Rate of recovery_rate from virus.
#' @export
#' @family Models
#' @aliases epiworld_seir
#' @details
#' The [initial_states] function allows the user to set the initial state of the
#' model. The user must provide a vector of proportions indicating the following
#' values: (1) Proportion of non-infected agents who are removed, and (2)
#' Proportion of exposed agents to be set as infected.
#' @returns
#' - The `ModelSEIR`function returns a model of class [epiworld_model].
#' @examples
#' model_seir <- ModelSEIR(name = "COVID-19", prevalence = 0.01,
#'   transmission_rate = 0.9, recovery_rate = 0.1, incubation_days = 4)
#'
#' # Adding a small world population
#' agents_smallworld(
#'   model_seir,
#'   n = 1000,
#'   k = 5,
#'   d = FALSE,
#'   p = .01
#' )
#'
#' # Running and printing
#' run(model_seir, ndays = 100, seed = 1912)
#' model_seir
#'
#' plot(model_seir, main = "SEIR Model")
#' @seealso epiworld-methods
ModelSEIR <- function(
    name,
    prevalence,
    transmission_rate,
    incubation_days,
    recovery_rate
    ) {
  # Check input parameters
  stopifnot_string(name)
  stopifnot_double(prevalence)
  stopifnot_double(transmission_rate)
  stopifnot_double(incubation_days)
  stopifnot_double(recovery_rate)

  structure(
    ModelSEIR_cpp(name, prevalence, transmission_rate, incubation_days, recovery_rate),
    class = c("epiworld_seir", "epiworld_model")
  )

}