functional_resistance: Compute functional resistance and stability-adjusted...

In r4pde: Tools for Quantitative Plant Disease Epidemiology

Compute functional resistance and stability-adjusted functional resistance

Description

Computes a functional resistance index (FRI) relative to a reference genotype curve. Optionally adjusts FRI by a functional instability penalty to calculate a stability-adjusted functional resistance index (SAFRI). Supports grouping genotypes into classes based on quantiles, clustering, or bootstrap-supported differences.

Usage

functional_resistance(
  object,
  instability = NULL,
  reference,
  lambda = 1,
  method = c("positive_area", "l2_difference"),
  scale_nfi = FALSE,
  n_groups = 4,
  group_method = c("none", "quantile", "bootstrap", "clustering"),
  time_var = NULL,
  genotype_var = NULL,
  n_boot = 1000,
  ci_level = 0.95,
  clustering_method = c("hclust", "kmeans"),
  adjust_by = NULL,
  reference_within_group = FALSE,
  group_within_adjust_by = TRUE,
  ...
)

Arguments

object	An object of class functional_curves.
instability	Optional output from functional_instability().
reference	Character string naming the reference genotype, or a named vector if reference_within_group = TRUE.
lambda	Numeric penalty weight for instability. Default is 1.
method	Character string for distance method.
scale_nfi	Logical; if TRUE, normalizes nFI to a 0-1 scale before applying penalty.
n_groups	Integer number of classes to group into.
group_method	Character string for the grouping method.
time_var	Optional variable name overrides.
genotype_var	Optional variable name overrides.
n_boot	Integer number of bootstrap iterations.
ci_level	Numeric confidence level for bootstrap intervals.
clustering_method	Character string for clustering method if group_method = "clustering".
adjust_by	Optional character string naming a genotype-level covariate to stratify by.
reference_within_group	Logical; if TRUE, the reference is evaluated within each adjust_by group.
group_within_adjust_by	Logical; if TRUE, resistance classes are assigned within each adjust_by group.
...	Additional arguments.

Value

A list with a table containing genotype, FRI, nFI, SAFRI, rank, and classes, and optionally bootstrap results.

Examples

## Not run: 
fr <- functional_resistance(
  fc,
  reference = "Susceptible",
  group_method = "bootstrap"
)
print(fr)

## End(Not run)

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