R/AUDPC_2_points.R

In AlvesKS/epifitter: Analysis and Simulation of Plant Disease Progress Curves

AUDPC_2_points <- function(time, y0, yT) {
  if (missing(time)) {
    stop("Missing 'time' value")
  }
  if (missing(y0)) {
    stop("Missing 'y0' value")
  }
  if (missing(yT)) {
    stop("Missing 'yT' value")
  }
  if (!all(is.numeric(time), is.numeric(y0), is.numeric(yT))) {
    stop("All values must be numeric")
  }
  if ((y0 < 0 || y0 >= 1) || (yT < y0 || yT >= 1)) {
    stop("y0 and yT must be between 0 and <1 and yT must be > y0")
  }
  # eqn. 3 from Jeger and Viljanen-Rollinson (2001), rate parameter r
  r <- (log(yT / (1 - yT)) - log(y0 / (1 - y0))) / time

  # eqn. 2 from Jeger and Viljanen-Rollinson (2001), AUDPC estimation
  return(time + log(y0 / yT) / r)
}