R Observatory: Metrics for MetabolSSMF version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MetabolSSMF

0.1.0

Simplex-Structured Matrix Factorisation for Metabolomics Analysis

0packages depend

1.9Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Wenxuan LiuFirst published 2025-03-051 releasesCRAN page ↗

Provides a framework to perform soft clustering using simplex-structured matrix factorisation (SSMF). The package contains a set of functions for determining the optimal number of prototypes, the optimal algorithmic parameters, the estimation confidence intervals and the diversity of clusters. Abdolali, Maryam & Gillis, Nicolas (2020) doi:10.1137/20M1354982.

Install

R (CRAN)Ubuntu (r2u)

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

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

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-metabolssmf

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

Health

CRAN checks

13OK

Slowest check: 2.7 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

8

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 44 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 80%
Documented parameters: 100%
Return-value docs: 100%
References docs: 33%

Downloads

1.9K

CRAN downloads in the past year

Rank #20,662 · ~5/day · ~160/mo

Releases R versions

Daily download trend is not available in this view yet.

11430 days

53690 days

1.9K1 year

Compare downloads with other packages →

Also on101 r2u

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (8)

LaplacesDemon NMF doParallel foreach iterators lsei mclust tidyr

LinkingTo (0)

none

Suggests (6)

knitr rmarkdown caroline ggsci BiocManager Biobase

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Wenxuan Liu

Author, Maintainer

Authors (3)

Wenxuan Liu

Author, Maintainer

Lorraine Brennan

Author

Thomas Brendan Murphy

Author

Listed in earlier versions (1)

Murphy

no longer listed · 0.1.0

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-03-05
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 325 KB / 6 files
Download size: 1.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MetabolSSMF")

Format

Liu, W., Brennan, L., & Murphy, T. B. (2025). MetabolSSMF: Simplex-Structured Matrix Factorisation for Metabolomics Analysis (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.MetabolSSMF

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 MetabolSSMF version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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