nmode's Git Repositories - Rnaught/blob - R/ID.R

   1 #' ID method
   2 #'
   3 #' This function implements a least squares estimation method of R0 due to
   4 #' Fisman et al. (PloS One, 2013). See details for implementation notes.
   5 #'
   6 #' The method is based on a straightforward incidence decay model. The estimate
   7 #' of R0 is the value which minimizes the sum of squares between observed case
   8 #' counts and cases counts 'expected' under the model.
   9 #'
  10 #' This method is based on an approximation of the SIR model, which is most
  11 #' valid at the beginning of an epidemic. The method assumes that the mean of
  12 #' the serial distribution (sometimes called the serial interval) is known. The
  13 #' final estimate can be quite sensitive to this value, so sensitivity testing
  14 #' is strongly recommended. Users should be careful about units of time (e.g.,
  15 #' are counts observed daily or weekly?) when implementing.
  16 #'
  17 #' @param NT Vector of case counts.
  18 #' @param mu Mean of the serial distribution. This needs to match case counts
  19 #'           in time units. For example, if case counts are weekly and the
  20 #'           serial distribution has a mean of seven days, then \code{mu} should
  21 #'           be set to one. If case counts are daily and the serial distribution
  22 #'           has a mean of seven days, then \code{mu} should be set to seven.
  23 #'
  24 #' @return \code{ID} returns a single value, the estimate of R0.
  25 #'
  26 #' @examples
  27 #' # Weekly data:
  28 #' NT <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4)
  29 #'
  30 #' # Obtain R0 when the serial distribution has a mean of five days.
  31 #' ID(NT, mu = 5 / 7)
  32 #'
  33 #' # Obtain R0 when the serial distribution has a mean of three days.
  34 #' ID(NT, mu = 3 / 7)
  35 #'
  36 #' @export
  37 ID <- function(NT, mu) {
  38   NT <- as.numeric(NT)
  39   TT <- length(NT)
  40   s <- (1:TT) / mu
  41   y <- log(NT) / s
  42
  43   R0_ID <- exp(sum(y) / TT)
  44
  45   return(R0_ID)
  46 }