Ckmeans.1d.dp: Optimal, Fast, and Reproducible Univariate Clustering

Fast, optimal, and reproducible weighted univariate clustering by dynamic programming. Four problem are solved, including univariate k-means (Wang & Song 2011) <doi:10.32614/RJ-2011-015> (Song & Zhong 2020) <doi:10.1093/bioinformatics/btaa613>, k-median, k-segments, and multi-channel weighted k-means. Dynamic programming is used to minimize the sum of (weighted) within-cluster distances using respective metrics. Its advantage over heuristic clustering in efficiency and accuracy is pronounced at a large number of clusters. Weighted k-means can also process time series to perform peak calling. Multi-channel weighted k-means groups multiple univariate signals into k clusters. An auxiliary function generates histograms adaptive to patterns in data. This package provides a powerful set of tools for univariate data analysis with guaranteed optimality, efficiency, and reproducibility.

Version: 4.3.3
Imports: Rcpp, Rdpack (≥ 0.6-1)
LinkingTo: Rcpp
Suggests: testthat, knitr, rmarkdown
Published: 2020-07-22
Author: Joe Song ORCID iD [aut, cre], Hua Zhong ORCID iD [aut], Haizhou Wang [aut]
Maintainer: Joe Song <joemsong at cs.nmsu.edu>
License: LGPL (≥ 3)
NeedsCompilation: yes
Citation: Ckmeans.1d.dp citation info
Materials: README NEWS
CRAN checks: Ckmeans.1d.dp results

Downloads:

Reference manual: Ckmeans.1d.dp.pdf
Vignettes: Tutorial: Optimal univariate clustering
Note: Weight scaling in cluster analysis
Tutorial: Adaptive versus regular histograms
Package source: Ckmeans.1d.dp_4.3.3.tar.gz
Windows binaries: r-devel: Ckmeans.1d.dp_4.3.3.zip, r-release: Ckmeans.1d.dp_4.3.3.zip, r-oldrel: Ckmeans.1d.dp_4.3.3.zip
macOS binaries: r-release: Ckmeans.1d.dp_4.3.3.tgz, r-oldrel: Ckmeans.1d.dp_4.3.3.tgz
Old sources: Ckmeans.1d.dp archive

Reverse dependencies:

Reverse depends: GenomicOZone
Reverse imports: emba, weitrix
Reverse suggests: DiffXTables, FunChisq, GridOnClusters, vip, xgboost

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