R Observatory: Metrics for SpNMF version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SpNMF

0.1.1Package record

Supervised NMF

0packages depend

2.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Yun CaiCRAN page ↗

Non-negative Matrix Factorization(NMF) is a powerful tool for identifying the key features of microbial communities and a dimension-reduction method. When we are interested in the differences between the structures of two groups of communities, supervised NMF(Yun Cai, Hong Gu and Tobby Kenney (2017),doi:10.1186/s40168-017-0323-1) provides a better way to do this, while retaining all the advantages of NMF -- such as interpretability, and being based on a simple biological intuition.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)

install.packages("SpNMF", 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-spnmf

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

# 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-SpNMF

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

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 1.1 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 0.1.1

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 4
Examples that run: 100%4 run in a plain check
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 75%

How these are measured

Downloads

2.1K

CRAN downloads in the past year

Rank #23,326 · ~6/day · ~174/mo

Releases R versions

Daily download trend is not available in this view yet.

18830 days

56290 days

2.1K1 year

Compare downloads with other packages →

Also on64 r2u

How downloads are counted

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Installing SpNMF adds 33 packages (15 with compiled code, 33 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, colorspace 2.0 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 3.2.3

Imports (2)

NMFstats

LinkingTo (0)

none

Suggests (0)

none

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)

Yun Cai

Author, Maintainer since 0.1.0 (2018)

Hong Gu

Author · added in 0.1.1

Toby Kenney

Author · added in 0.1.1

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
0.1.1Latest
record
2018-10-03 · current release · diff ↗
0.1.0
record
2018-10-01
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-10-01
Total releases: 2 / 8 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.2.3
Bundled data: 147 KB / 1 file
Download size: 155 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SpNMF")

Format

Cai, Y., Gu, H., & Kenney, T. (2018). SpNMF: Supervised NMF (Version 0.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.SpNMF

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 SpNMF version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →