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Compute functional resistance and stability-adjusted functional resistance

Source: R/functional_resistance.R
functional_resistance.Rd

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

if (FALSE) { # \dontrun{
fr <- functional_resistance(
  fc,
  reference = "Susceptible",
  group_method = "bootstrap"
)
print(fr)
} # }