R/estimate.R0.R

In covid19br/now_fcts: Auxiliary functions for analyzing COVID-19 data from different sources

#' Estimating R accounting for uncertainty on the serial interval distribution
#'
#' @param novos.casos vetor com novos casos
#' @param day0 day to start the analysis
#' @param delay atraso
#' @param ... outros parâmetros
#'
#' @details The mean of the SI comes from a Normal(4.8, 0.71), truncated at 3.8 and 6.1
#' the sd of the SI comes from  a Normal(2.3, 0.58), truncated at 1.6 and 3.5
#'
#' @importFrom EpiEstim make_config estimate_R
#' @export
#'
estimate.R0 <- function(novos.casos, day0 = 8, delay = 7, ...) {
    config <- make_config(list(si_parametric_distr = "L",
                               mean_si = 4.8, std_mean_si = 0.71,
                               min_mean_si = 3.8, max_mean_si = 6.1,
                               std_si = 2.3, std_std_si = 0.58,
                               min_std_si = 1.6, max_std_si = 3.5,
                               t_start = seq(day0,length(novos.casos) - delay),
                               t_end = seq(delay + day0,length(novos.casos))))
    estimate_R(novos.casos, method = "uncertain_si", config = config)
}