Adding missing R and man files

R/ModelSIRD.R

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+#' SIRD model
+#' @param name String. Name of the virus.
+#' 
+#' Susceptible-Infected-Recovered-Deceased model ([wiki](https://en.wikipedia.org/w/index.php?title=Compartmental_models_in_epidemiology&oldid=1166587407#The_SIRD_model)).
+#' 
+#' @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 recovery_rate Numeric scalar between 0 and 1. Rate of recovery_rate from virus. 
+#' @param death_rate Numeric scalar between 0 and 1. Rate of death from virus.
+#' @param x Object of class SIR. 
+#' @param ... Additional arguments passed to [graphics::plot].
+#' @export
+#' @family Models
+#' @aliases epiworld_sir
+#' @returns
+#' - The `ModelSIR` function returns a model of class [epiworld_model].
+#' @examples 
+#' model_sird <- ModelSIRD(
+#'  name              = "COVID-19",
+#'  prevalence        = 0.01, 
+#'  transmission_rate = 0.9,
+#'  recovery_rate     = 0.1,
+#'  death_rate        = 0.01
+#' )
+#' 
+#' # Adding a small world population
+#' agents_smallworld(
+#'   model_sird,
+#'   n = 1000,
+#'   k = 5,
+#'   d = FALSE,
+#'   p = .01
+#'   )
+#'   
+#' # Running and printing
+#' run(model_sird, ndays = 100, seed = 1912)
+#' model_sird
+#' 
+#' # Plotting
+#' plot(model_sird)
+#' @seealso epiworld-methods
+ModelSIRD <- function(
+    name, prevalence, transmission_rate, recovery_rate, death_rate
+) {
+
+  structure(
+    ModelSIRD_cpp(name, prevalence, transmission_rate, recovery_rate, death_rate),
+    class = c("epiworld_sird", "epiworld_model")
+  )
+
+}
+
+#' @rdname ModelSIRD
+#' @export
+#' @returns 
+#' - The `plot` function returns a plot of the SIRD model of class 
+#' [epiworld_model].
+#' @param main Title of the plot
+plot.epiworld_sird <- function(x, main = get_name(x), ...) { # col = NULL
+ plot_epi(x, main = main, ...)
+}
+