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@@ -0,0 +1,46 @@ +#' ID method +#' +#' This function implements a least squares estimation method of R0 due to +#' Fisman et al. (PloS One, 2013). See details for implementation notes. +#' +#' The method is based on a straightforward incidence decay model. The estimate +#' of R0 is the value which minimizes the sum of squares between observed case +#' counts and cases counts 'expected' under the model. +#' +#' This method is based on an approximation of the SIR model, which is most +#' valid at the beginning of an epidemic. The method assumes that the mean of +#' the serial distribution (sometimes called the serial interval) is known. The +#' final estimate can be quite sensitive to this value, so sensitivity testing +#' is strongly recommended. Users should be careful about units of time (e.g., +#' are counts observed daily or weekly?) when implementing. +#' +#' @param NT Vector of case counts. +#' @param mu Mean of the serial distribution. This needs to match case counts +#' in time units. For example, if case counts are weekly and the +#' serial distribution has a mean of seven days, then \code{mu} should +#' be set to one. If case counts are daily and the serial distribution +#' has a mean of seven days, then \code{mu} should be set to seven. +#' +#' @return \code{ID} returns a single value, the estimate of R0. +#' +#' @examples +#' # Weekly data: +#' NT <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4) +#' +#' # Obtain R0 when the serial distribution has a mean of five days. +#' ID(NT, mu = 5 / 7) +#' +#' # Obtain R0 when the serial distribution has a mean of three days. +#' ID(NT, mu = 3 / 7) +#' +#' @export +ID <- function(NT, mu) { + NT <- as.numeric(NT) + TT <- length(NT) + s <- (1:TT) / mu + y <- log(NT) / s + + R0_ID <- exp(sum(y) / TT) + + return(R0_ID) +} |