R Observatory: Metrics for MetabolSSMF version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MetabolSSMF

0.1.0Package record

Simplex-Structured Matrix Factorisation for Metabolomics Analysis

0packages depend

2.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Wenxuan LiuCRAN 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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMEYes · 44 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 12
Examples that run: 20%1 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 83%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 33%

Vignettes (1)

MetabolSSMF HTML

How these are measured

Downloads

2.1K

CRAN downloads in the past year

Rank #22,380 · ~6/day · ~176/mo

Releases R versions

Daily download trend is not available in this view yet.

22330 days

59090 days

2.1K1 year

Compare downloads with other packages →

Also on71 r2u

How downloads are counted

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing MetabolSSMF adds 45 packages (23 with compiled code, 41 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, mclust 2.7 MB. 1 more not on CRAN is not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Wenxuan Liu

Author, Maintainer since 0.1.0 (2025)

Lorraine Brennan

Author

Thomas Brendan Murphy

Author

Listed in earlier versions (1)

Murphy

no longer listed · 0.1.0

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.1.0Latest
record
2025-03-05 · current release
R
R 4.4.0 released · 2024-04-24

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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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