build.iknn.graphs.and.selectk: Build iKNN Graphs and Select a Neighborhood Size

In dgraphs: Data-Derived Graph Construction Utilities

Build iKNN Graphs and Select a Neighborhood Size

Description

Builds an iKNN graph sequence and selects k from structural edit-distance stability, label-mixing stability, or both.

Usage

build.iknn.graphs.and.selectk(
  X,
  kmin,
  kmax,
  method = c("both", "edit", "mixing", "none"),
  pca.dim = 100,
  variance.explained = 0.99,
  trim.disconnected = TRUE,
  edit.min.lcc.frac = 1,
  edit.eps = 0.05,
  labels = NULL,
  perm.blocks = NULL,
  mixing.metric = c("homophily.effect", "homophily.z", "homophily.adjusted",
    "assortativity.effect", "assortativity.z", "homophily", "assortativity",
    "conductance.median", "conductance.wmean"),
  mixing.min.lcc.frac = 0.98,
  mixing.eps = 0.05,
  mixing.require.local.extremum = TRUE,
  mixing.window = 1L,
  n.perm = 200L,
  use.edge.weights = TRUE,
  weights.are.edge.lengths = FALSE,
  affinity.method = c("exp", "inv"),
  affinity.sigma = NULL,
  affinity.sigma.from = c("k.cc.mixing", "k.max.lcc", "k.trim"),
  affinity.eps = 1e-08,
  simplify.multiple = TRUE,
  seed = 1L,
  n.cores = 1L,
  verbose = TRUE,
  ...
)

Arguments

X	Numeric observation-by-feature matrix.
kmin, kmax	Minimum and maximum neighborhood sizes.
method	Selection criterion.
pca.dim, variance.explained	PCA controls forwarded to create.iknn.graphs().
trim.disconnected	Logical; trim to a largest connected component when the requested connectivity tail is absent.
edit.min.lcc.frac, edit.eps	Connectivity and tolerance controls for edit-distance selection.
labels, perm.blocks	Optional labels and permutation blocks for mixing selection.
mixing.metric, mixing.min.lcc.frac, mixing.eps	Mixing criterion, connectivity threshold, and tolerance.
mixing.require.local.extremum, mixing.window	Local-extremum controls for the mixing curve.
n.perm	Number of label permutations.
use.edge.weights, weights.are.edge.lengths	Edge-weight interpretation.
affinity.method, affinity.sigma, affinity.sigma.from, affinity.eps	Controls for converting edge lengths to affinities.
simplify.multiple	Logical; simplify loops and multiple edges.
seed	Random seed.
n.cores	Number of worker processes.
verbose	Logical; report progress.
...	Additional arguments forwarded to create.iknn.graphs().

Value

An object of class "build_iknn_graphs_and_selectk" containing the graph sequence, connectivity diagnostics, selection curves, selected neighborhood sizes, trimming metadata, and call parameters.

dgraphs documentation built on Aug. 21, 2026, 1:08 a.m.