speakeasyR: Fast and Robust Multi-Scale Graph Clustering

A graph community detection algorithm that aims to be performant on large graphs and robust, returning consistent results across runs. SpeakEasy 2 (SE2), the underlying algorithm, is described in Chris Gaiteri, David R. Connell & Faraz A. Sultan et al. (2023) <doi:10.1186/s13059-023-03062-0>. The core algorithm is written in 'C', providing speed and keeping the memory requirements low. This implementation can take advantage of multiple computing cores without increasing memory usage. SE2 can detect community structure across scales, making it a good choice for biological data, which often has hierarchical structure. Graphs can be passed to the algorithm as adjacency matrices using base 'R' matrices, the 'Matrix' library, 'igraph' graphs, or any data that can be coerced into a matrix.

Version:	0.1.8
Imports:	Matrix, methods
Suggests:	igraph, scRNAseq, SummarizedExperiment, knitr, rmarkdown, testthat (≥ 3.0.0)
Published:	2025-09-30
DOI:	10.32614/CRAN.package.speakeasyR
Author:	David Connell [aut, cre, cph], Chris Gaiteri [cph] (Author of original SpeakEasy 2 algorithm.), Gábor Csárdi [cph, ctb] (Author of igraph C library.), Tamás Nepusz [cph, ctb] (Author of igraph C library.), Szabolcs Horvát [cph, ctb] (Author of igraph C library.), Vincent Traag [cph, ctb] (Author of igraph C library.), Fabio Zanini [cph, ctb] (Author of igraph C library.), Daniel Noom [cph, ctb] (Author of igraph C library.), The igraph development team [cph] (Copyright holder of igraph C library.), Free Software Foundation, Inc. [cph] (Copyright holder of GPL licenses.), Ross Ihaka [cph, ctb] (Author of Mathlib.), The R Development Core Team [cph] (Copyright holder of Mathlib.), Royal Statistical Society [cph] (Copyright holder of Mathlib.), The R Core Team [cph] (Copyright holder of Mathlib.), The Regents of the University of California [cph] (Copyright holder of stdlib's qsort.), Timothy Davis [cph, ctb] (Author of CXSPARSE (cs).), Richard Lehoucq [cph, ctb] (Author of arpack.), Danny Scrensen [cph, ctb] (Author of arpack and lapack.), Phuong Vu [cph, ctb] (Author of arpack.), Chao Yang [cph, ctb] (Author of arpack.), Allan Cornet [cph, ctb] (Author of arpack.), Sylvestre Ledru [cph, ctb] (Author of arpack.), Chao Yang [cph, ctb] (Author of arpack.), Rice University [cph] (Copyright holder of arpack.), Scilab Enterprises [cph] (Copyright holder of arpack-ng.), Melissa O'Neill [cph, ctb] (Author of PCG random number generator.), Steven Johnson [cph, ctb] (Author of ax_pthread.), Daniel G. [cph, ctb] (Author of ax_pthread.), Marc Stevens [cph, ctb] (Author of ax_pthread.), Minh Nguyen [cph, ctb] (Author of ax_pthread.), Elliot Paquette [cph, ctb] (Contributor to igraph.), Pascal Pons [cph, ctb] (Contributor to igraph.), Jordi Hermoso [cph, ctb] (Contributor to arpack.), Sébastien Fabbro [cph, ctb] (Contributor to arpack.), Shinya Tasaki [cph, ctb] (Provided code used in the gene clustering example.)
Maintainer:	David Connell <david32 at dcon.addy.io>
BugReports:	https://github.com/SpeakEasy-2/speakeasyR/issues
License:	GPL (≥ 3)
URL:	https://github.com/SpeakEasy-2/speakeasyR
NeedsCompilation:	yes
SystemRequirements:	arpack (optional)
Materials:	README, NEWS
CRAN checks:	speakeasyR results

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