diff --git a/R/ModelSURVD.R b/R/ModelSURVD.R deleted file mode 100644 index 494ea767..00000000 --- a/R/ModelSURVD.R +++ /dev/null @@ -1,88 +0,0 @@ -#' SURVD model -#' -#' -#' @param name String. Name of the virus. -#' @param prevalence Initial number of individuals with the virus. -#' @param efficacy_vax Double. Efficacy of the vaccine. -#' (1 - P(acquire the disease)). -#' @param latent_period Double. Shape parameter of a 'Gamma(latent_period, 1)' -#' distribution. This coincides with the expected number of latent days. -#' @param infect_period Double. Shape parameter of a 'Gamma(infected_period, 1)' -#' distribution. This coincides with the expected number of infectious days. -#' @param prob_symptoms Double. Probability of generating symptoms. -#' @param prop_vaccinated Double. Probability of vaccination. Coincides with -#' the initial prevalence of vaccinated individuals. -#' @param prop_vax_redux_transm Double. Factor by which the vaccine reduces -#' transmissibility. -#' @param prop_vax_redux_infect Double. Factor by which the vaccine reduces -#' the chances of becoming infected. -#' @param surveillance_prob Double. Probability of testing an agent. -#' @param transmission_rate Double. Raw transmission probability. -#' @param prob_death Double. Raw probability of death for symptomatic -#' individuals. -#' @param prob_noreinfect Double. Probability of no re-infection. -#' @param x Object of class SURV. -#' @param ... Currently ignore. -#' @export -#' @family Models -#' @aliases epiworld_survd -#' @returns -#' - The `ModelSURVD`function returns a model of class [epiworld_model]. -#' @examples -#' model_survd <- ModelSURVD( -#' name = "COVID-19", -#' prevalence = 20, -#' efficacy_vax = 0.6, -#' latent_period = 4, -#' infect_period = 5, -#' prob_symptoms = 0.5, -#' prop_vaccinated = 0.7, -#' prop_vax_redux_transm = 0.8, -#' prop_vax_redux_infect = 0.95, -#' surveillance_prob = 0.1, -#' transmission_rate = 0.2, -#' prob_death = 0.001, -#' prob_noreinfect = 0.5 -#' ) -#' -#' # Adding a small world population -#' agents_smallworld( -#' model_survd, -#' n = 10000, -#' k = 5, -#' d = FALSE, -#' p = .01 -#' ) -#' -#' # Running and printing -#' run(model_survd, ndays = 100, seed = 1912) -#' model_survd -#' -#' # Plotting -#' plot(model_survd, main = "SURVD Model") -#' -#' @seealso epiworld-methods -ModelSURVD <- function( - name, prevalence, efficacy_vax, latent_period, infect_period, prob_symptoms, - prop_vaccinated, prop_vax_redux_transm, prop_vax_redux_infect, - surveillance_prob, transmission_rate, prob_death, prob_noreinfect -) { - - structure( - ModelSURVD_cpp(name, prevalence, efficacy_vax, latent_period, infect_period, - prob_symptoms, prop_vaccinated, prop_vax_redux_transm, - prop_vax_redux_infect, surveillance_prob, transmission_rate, - prob_death, prob_noreinfect), - class = c("epiworld_survd", "epiworld_model") - ) - -} - -#' @rdname ModelSURVD -#' @export -#' @returns The `plot` function returns a plot of the SURV model of class -#' [epiworld_model]. -#' @param main Title of the plot. -plot.epiworld_survd <- function(x, main = get_name(x), ...) { # col = NULL - plot_epi(x, main = main, ...) -}