Area under the disease progress curve

Calculate the area under a disease progress curve using the trapezoidal method.

Usage

AUDPC(
  time,
  y,
  y_proportion = TRUE,
  type = "absolute",
  aggregate = c("mean", "median", "none")
)

time: A numeric vector of assessment times.
y: A numeric vector of disease intensity values.
y_proportion: Logical. Are the `y` values expressed as proportions?
type: Either `"absolute"` or `"relative"`.
aggregate: How to handle multiple observations at the same time point. The default, `"mean"`, averages replicated observations before calculating area. `"median"` uses the median and `"none"` requires unique time values.

A numeric scalar with the AUDPC value.

Madden, L. V., Hughes, G., and van den Bosch, F. (2007). The Study of Plant Disease Epidemics. American Phytopathological Society.

epi <- sim_logistic(N = 30, y0 = 0.01, dt = 5, r = 0.3, alpha = 0.5, n = 1)
AUDPC(time = epi$time, y = epi$y, y_proportion = TRUE)
#> [1] 14.79107