functional_summary: Summarize Disease Suppression Profiles

In r4pde: Tools for Quantitative Plant Disease Epidemiology

Summarize Disease Suppression Profiles

Description

Extracts functional descriptors from Disease Suppression Profiles (DSPs).

Usage

functional_summary(
  object,
  time = "time",
  response = "DSP",
  treatment = "treatment",
  group = NULL,
  threshold = 0,
  positive_only = TRUE
)

Arguments

object	An object of class "functional_dsp" or a data frame with a DSP column.
time	Character string naming the time column.
response	Character string naming the DSP column.
treatment	Character string naming the treatment column.
group	Optional character vector of grouping variables.
threshold	Numeric; minimum suppression threshold for calculating persistence. Default is 0.
positive_only	Logical; if TRUE, negative DSP values are set to 0 before area/centroid calculations. Default is TRUE.

Value

A tibble with one row per group/treatment containing:

• protected_area: Trapezoidal integral of DSP(t).

• mean_suppression: Temporal mean of DSP(t).

• max_suppression: Maximum value of DSP(t).

• time_max_suppression: Time at which maximum suppression occurs.

• persistence: Total duration where DSP(t) > threshold.

• centroid: Temporal centroid defined as \int t \cdot DSP(t) dt / \int DSP(t) dt.

• energy: Integral of DSP(t)^2.

• early_area, mid_area, late_area: Protected area in the first, second, and third tertiles of the time period.

• late_decline_slope: Slope of DSP(t) in the late period.

• n_time_points: Number of time points evaluated.

Examples

## Not run: 
# Using a generic data frame with custom column names
dat <- data.frame(
  DAA = c(0, 10, 20),
  fungicide = c("A", "A", "A"),
  contrast = c(0, 10, 0)
)
functional_summary(
  dat, 
  time = "DAA", 
  response = "contrast", 
  treatment = "fungicide"
)

## End(Not run)

r4pde documentation built on Sept. 8, 2026, 1:10 a.m.