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Area under the disease progress stairs

Source: R/AUDPS.R
AUDPS.Rd

Calculate the area under the disease progress stairs, an alternative to AUDPC that gives more balanced weight to the first and last observations.

Usage

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

Arguments

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.

Value

A numeric scalar with the AUDPS value.

References

Simko, I., and Piepho, H.-P. (2012). The area under the disease progress stairs: Calculation, advantage, and application. Phytopathology, 102, 381-389.

Examples

epi <- sim_logistic(N = 30, y0 = 0.01, dt = 5, r = 0.3, alpha = 0.5, n = 1)
AUDPS(time = epi$time, y = epi$y, y_proportion = TRUE)
#> [1] 17.2859