refine.linf.csts: Refine a dCST hierarchy by one level

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

Refine a dCST hierarchy by one level

Description

Selects well-supported leaf dominance-lineages and refines them by dropping the dominant feature(s) encoded in the parent label path and re-applying linf.csts to the remaining features. The resulting child labels are appended to the parent label using sep.

Low-support child lineages are handled by low.freq.policy. When low.freq.policy = "pure", rare buckets at depth >= 2 become parent-prefixed automatically via the hierarchical paste(parent, child, sep = sep).

Usage

refine.linf.csts(
  M,
  csts,
  n0 = 50,
  refinement.factor = 2,
  sep = "__",
  low.freq.policy = c("pure", "absorb"),
  rare.label = "RARE_DOMINANT",
  verbose = TRUE,
  backend = c("auto", "dense", "sparse")
)

Arguments

M	Numeric matrix (samples x features) used for refinement. Column names should match feature labels used in dCST names.
csts	A "linf.csts" object.
n0	Integer >= 1. Minimum support required to retain a child lineage (passed to linf.csts).
refinement.factor	Numeric > 0. Auto-refine parent lineages with support >= refinement.factor * n0.
sep	Character scalar used to concatenate hierarchical labels.
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 for rare buckets when low.freq.policy = "pure".
verbose	Logical. If TRUE, print progress information.
backend	Character. Matrix backend to use: "auto", "dense", or "sparse". The default "auto" inherits the backend from M or from csts when available.

Value

Updated "linf.csts" object with cst.depth increased by one and updated cell.label. Policy-specific views are stored in cell.label.rare and cell.label.absorb.

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