R Observatory: Metrics for speakeasyR version 0.1.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

speakeasyR

0.1.8

Fast and Robust Multi-Scale Graph Clustering

0packages depend

4Kdownloads / year

12.8%test coverage

13/13checks pass

Overview

About

Maintained by David ConnellFirst published 2024-06-188 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("speakeasyR", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("SpeakEasy-2/speakeasyR")

Development version from SpeakEasy-2/speakeasyR. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-speakeasyr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-speakeasyR

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-speakeasyR

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 5.7 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.15

12.8%

Coverage · measured lines

100%

Documentation · exports

2

Dependencies · direct

Check history

OK2026-08-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

WARNING2026-04-09
13 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 578 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

4K

CRAN downloads in the past year

Rank #18,025 · ~11/day · ~333/mo

Releases R versions

Daily download trend is not available in this view yet.

15530 days

61790 days

4K1 year

Compare downloads with other packages →

Also on447 r2u33 autocran

Repository

GitHub ↗ speakeasy-2/speakeasyr

3Stars

1Forks

0Open issues

0Open PRs

8Releases

172Commits

2Contributors

License GPL-3.0 · 172 commits · Last activity 2025-09-30

Stars over time

2024-08-21 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/speakeasy-2/speakeasyr on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Makefile

CRAN release process (1)

cran-comments.md

Git structural (1)

Submodules

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (2)

Matrixmethods

LinkingTo (0)

none

Suggests (6)

igraph scRNAseq SummarizedExperiment knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (34)

Maintainer (1)

David Connell

Author, Maintainer, Copyright holder

Authors (1)

David Connell

Author, Maintainer, Copyright holder

Contributors (24)

Allan Cornet

Copyright holder, Contributor · added in 0.1.2

Gábor Csárdi

Copyright holder, Contributor

Timothy Davis

Copyright holder, Contributor · added in 0.1.2

Sébastien Fabbro

Copyright holder, Contributor · added in 0.1.2

Daniel G.

Copyright holder, Contributor · added in 0.1.2

Jordi Hermoso

Copyright holder, Contributor · added in 0.1.2

Szabolcs Horvát

Copyright holder, Contributor

Ross Ihaka

Copyright holder, Contributor · added in 0.1.2

Show 16 more contributors

Steven Johnson

Copyright holder, Contributor · added in 0.1.2

Sylvestre Ledru

Copyright holder, Contributor · added in 0.1.2

Richard Lehoucq

Copyright holder, Contributor · added in 0.1.2

Tamás Nepusz

Copyright holder, Contributor

Minh Nguyen

Copyright holder, Contributor · added in 0.1.2

Daniel Noom

Copyright holder, Contributor

Melissa O'Neill

Copyright holder, Contributor · added in 0.1.2

Elliot Paquette

Copyright holder, Contributor · added in 0.1.2

Pascal Pons

Copyright holder, Contributor · added in 0.1.2

Danny Scrensen

Copyright holder, Contributor · added in 0.1.2

Marc Stevens

Copyright holder, Contributor · added in 0.1.2

Shinya Tasaki

Copyright holder, Contributor · added in 0.1.4

Vincent Traag

Copyright holder, Contributor

Phuong Vu

Copyright holder, Contributor · added in 0.1.2

Chao Yang

Copyright holder, Contributor · added in 0.1.2

Fabio Zanini

Copyright holder, Contributor

Copyright holders (34)

David Connell

Author, Maintainer, Copyright holder

Allan Cornet

Copyright holder, Contributor · added in 0.1.2

Gábor Csárdi

Copyright holder, Contributor

Timothy Davis

Copyright holder, Contributor · added in 0.1.2

Sébastien Fabbro

Copyright holder, Contributor · added in 0.1.2

Daniel G.

Copyright holder, Contributor · added in 0.1.2

Jordi Hermoso

Copyright holder, Contributor · added in 0.1.2

Szabolcs Horvát

Copyright holder, Contributor

Show 26 more copyright holders

Ross Ihaka

Copyright holder, Contributor · added in 0.1.2

Steven Johnson

Copyright holder, Contributor · added in 0.1.2

Sylvestre Ledru

Copyright holder, Contributor · added in 0.1.2

Richard Lehoucq

Copyright holder, Contributor · added in 0.1.2

Tamás Nepusz

Copyright holder, Contributor

Minh Nguyen

Copyright holder, Contributor · added in 0.1.2

Daniel Noom

Copyright holder, Contributor

Melissa O'Neill

Copyright holder, Contributor · added in 0.1.2

Elliot Paquette

Copyright holder, Contributor · added in 0.1.2

Pascal Pons

Copyright holder, Contributor · added in 0.1.2

Danny Scrensen

Copyright holder, Contributor · added in 0.1.2

Marc Stevens

Copyright holder, Contributor · added in 0.1.2

Shinya Tasaki

Copyright holder, Contributor · added in 0.1.4

Vincent Traag

Copyright holder, Contributor

Phuong Vu

Copyright holder, Contributor · added in 0.1.2

Chao Yang

Copyright holder, Contributor · added in 0.1.2

Fabio Zanini

Copyright holder, Contributor

Free Software Foundation, Inc.

Copyright holder · added in 0.1.2

Rice University

Copyright holder · added in 0.1.2

Royal Statistical Society

Copyright holder · added in 0.1.2

Scilab Enterprises

Copyright holder · added in 0.1.2

The R Core Team

Copyright holder · added in 0.1.2

The R Development Core Team

Copyright holder · added in 0.1.2

The Regents of the University of California

Copyright holder · added in 0.1.2

The igraph development team

Copyright holder · added in 0.1.2

Chris Gaiteri

Copyright holder

Package Timeline

8 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.8Latest
2025-09-30 · current release · diff ↗
0.1.7
2025-09-05 · diff ↗
0.1.6
2025-08-28 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.1.5
2025-04-03 · diff ↗
0.1.4
2024-09-25 · diff ↗
0.1.3
2024-08-20 · diff ↗
unarchivedReturned to CRAN
2024-08-20
archivedRemoved from CRAN
2024-08-19
issues were not corrected in time
0.1.2
2024-07-29 · diff ↗
unarchivedReturned to CRAN
2024-07-29
archivedRemoved from CRAN
2024-06-19
policy violations including misrepresentation of authorship The included sources such as 'glpk' and 'lapack' are not credited System versions are not looked for ASAN errors even in re-submission
0.1.0
2024-06-18
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-06-18
Total releases: 8 / 2 yrs
License: GPL (>= 3) OSI
Download size: 2.8 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("speakeasyR")

Format

Connell, D., Free Software Foundation, Inc., Rice University, Royal Statistical Society, Scilab Enterprises, The R Core Team, The R Development Core Team, The Regents of the University of California, The igraph development team, Cornet, A., Csárdi, G., Davis, T., Fabbro, S., G., D., Gaiteri, C., Hermoso, J., Horvát, S., Ihaka, R., Johnson, S., Ledru, S., Lehoucq, R., Nepusz, T., Nguyen, M., Noom, D., O'Neill, M., Paquette, E., Pons, P., Scrensen, D., Stevens, M., Tasaki, S., Traag, V., Vu, P., Yang, C., & Zanini, F. (2025). speakeasyR: Fast and Robust Multi-Scale Graph Clustering (Version 0.1.8) [Computer software]. https://doi.org/10.32614/CRAN.package.speakeasyR

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for speakeasyR version 0.1.8 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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