linf.csts: Truncated dominant community state types with configurable...

In linf: L-Infinity Normalization and Dominant Community State Types

Truncated dominant community state types with configurable low-support handling

Description

Forms provisional depth-1 dominance sample sets from the dominant feature of each sample and then applies the minimum support threshold n0. Sets with fewer than n0 samples are handled according to low.freq.policy:

• "pure": retain only sets with support >= n0 as named dCSTs and collapse all low-support sets into rare.label.

• "absorb": reassign each low-support sample to the retained state with the largest value among the retained features (ties handled by tie.method).

Usage

linf.csts(
  S,
  feature.ids = NULL,
  feature.labels = NULL,
  n0 = 50,
  low.freq.policy = c("pure", "absorb"),
  rare.label = "RARE_DOMINANT",
  tie.method = c("first", "random", "error"),
  return.diagnostics = FALSE,
  return.landmarks = FALSE,
  landmark.types = c("endpoint.max", "endpoint.min"),
  landmark.view = c("active", "rare", "absorb"),
  backend = c("auto", "dense", "sparse")
)

Arguments

S	Numeric matrix (samples x features), typically L-infinity relatives.
feature.ids	Optional character vector of stable feature identifiers, length ncol(S).
feature.labels	Optional character vector of display labels, length ncol(S).
n0	Integer >= 1. Minimum support required to retain a dominance sample set.
low.freq.policy	Character. One of "pure" or "absorb". Default: "pure". The legacy value "rare" is still accepted as a deprecated alias for "pure".
rare.label	Character scalar used when low.freq.policy = "pure". Default: "RARE_DOMINANT".
tie.method	Character. Tie handling passed to linf.cells() and used during absorb reassignment ("first", "random", "error").
return.diagnostics	Logical. If TRUE, return reassignment diagnostics.
return.landmarks	Logical. If TRUE, attach a depth-1 landmark summary computed by linf.landmarks.
landmark.types	Character vector of landmark types passed to linf.landmarks when return.landmarks = TRUE.
landmark.view	Character. Landmark view passed to linf.landmarks when return.landmarks = TRUE.
backend	Character. Matrix backend to use: "auto", "dense", or "sparse". The default "auto" preserves sparse input and otherwise uses the dense path.

Value

List with:

• cell.index, cell.id, cell.label: active labeling per low.freq.policy

• cell.index.rare, cell.id.rare, cell.label.rare

• cell.index.absorb, cell.id.absorb, cell.label.absorb

• kept.cells.idx, kept.cells.id, kept.cells.lbl

• raw.index, raw.id, raw.label

• feature.ids, feature.labels

• size.table, size.table.id

• n0, low.freq.policy, rare.label

• diagnostics (if return.diagnostics = TRUE)

• landmarks (if return.landmarks = TRUE)

linf documentation built on Aug. 5, 2026, 9:08 a.m.