ABCdist.SingleInMultiple: Single-source ABC with distance accumulation

In MosaiClusteR: An Umbrella Framework for Multi-Source and Multi-Omics Clustering

Single-source ABC with distance accumulation

Description

A variant of ABCpp.SingleInMultiple that accumulates the mean scaled pairwise distance between co-selected objects across iterations, yielding a [0, 1] dissimilarity matrix that M_ABCdist fuses across sources.

Usage

ABCdist.SingleInMultiple(
  data,
  distmeasure = "euclidean",
  weighting = "var",
  normalize = NULL,
  gr = c(),
  bag = TRUE,
  numsim = 1000,
  numvar = 100,
  linkage = "ward.D",
  NC = NULL,
  mds = FALSE,
  nfeat = NULL,
  nugget_type = "between",
  nugget_args = list()
)

Arguments

data	Numeric matrix with objects (samples) in rows and features in columns (the MosaiClusteR convention; transposed internally to the features-by-objects layout of the original engine).
distmeasure	Distance measure passed to Distance.
weighting	"var", "cv", "nugget" or equal.
normalize	Optional normalisation (see Normalization).
gr	Unused; kept for interface compatibility.
bag	Logical; bootstrap the objects each iteration (Step 2).
numsim	Number of iterations R.
numvar	Kept for backward compatibility; superseded by nfeat.
linkage	Agglomeration method for fastcluster::hclust.
NC	Base-cluster count (NULL = \lfloor\sqrt{N}\rfloor).
mds	Unused placeholder.
nfeat	Optional feature-subsample size. NULL (default) uses the classic g=\lfloor\sqrt{G}\rfloor; a value \ge 1 sets an absolute count (raise it for low-dimensional sources where most features matter).
nugget_type, nugget_args	Passed to the data-nugget weighting when weighting = "nugget".

Value

A list with D (N \times N dissimilarity), NC and ng (per-iteration feature count); if mds = TRUE also mds_coords.

References

\insertCite

Amaratunga2008MosaiClusteR

See Also

M_ABCdist, ABCpp.SingleInMultiple

Examples

data(mosaic_toy)
out <- ABCdist.SingleInMultiple(mosaic_toy$List[[1]], numsim = 40)
dim(out$D)

MosaiClusteR documentation built on Oct. 25, 2026, 1:08 a.m.