SpNMF

0.1.1

Supervised NMF

0packages depend

2Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Yun CaiFirst published 2018-10-012 releasesCRAN 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.

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

Slowest check: 1.1 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

None

Vignettes

README

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

CRAN downloads in the past year

Rank #21,356 · ~6/day · ~168/mo

Releases R versions

Daily download trend is not available in this view yet.

21230 days

56090 days

2K1 year

Compare downloads with other packages →

Also on88 r2u

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

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.

Code & Tests

Code Composition

R 373 (68%)Rd 172 (32%)

Code characteristics

Cyclomatic complexity: 13.0 median / 14 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

3 0 exported

Complexity

9.3 avg / 14 max

Call network

3 nodes / 1 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (3)

Maintainer (1)

Yun Cai

Author, Maintainer

Authors (3)

Yun Cai

Author, Maintainer

Hong Gu

Author · added in 0.1.1

Toby Kenney

Author · added in 0.1.1

Package Timeline

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

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
2018-10-03 · current release · diff ↗
0.1.0
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
Installed size: not tracked yet
With dependencies: not tracked yet