R Observatory: Metrics for vrnmf version 1.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

vrnmf

1.0.2

Volume-Regularized Structured Matrix Factorization

0packages depend

2.6Kdownloads / year

17.1%test coverage

13/13checks pass

Overview

About

Maintained by Evan BiederstedtFirst published 2021-08-203 releasesCRAN page ↗GitHub ↗

Implements a set of routines to perform structured matrix factorization with minimum volume constraints. The NMF procedure decomposes a matrix X into a product C * D. Given conditions such that the matrix C is non-negative and has sufficiently spread columns, then volume minimization of a matrix D delivers a correct and unique, up to a scale and permutation, solution (C, D). This package provides both an implementation of volume-regularized NMF and "anchor-free" NMF, whereby the standard NMF problem is reformulated in the covariance domain. This algorithm was applied in Vladimir B. Seplyarskiy Ruslan A. Soldatov, et al. "Population sequencing data reveal a compendium of mutational processes in the human germ line". Science, 12 Aug 2021. doi:10.1126/science.aba7408. This package interacts with data available through the 'simulatedNMF' package, which is available in a 'drat' repository. To access this data package, see the instructions at https://github.com/kharchenkolab/vrnmf. The size of the 'simulatedNMF' package is approximately 8 MB.

Install

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

install.packages("vrnmf", 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("kharchenkolab/vrnmf")

Development version from kharchenkolab/vrnmf. 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-vrnmf

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-vrnmf

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-vrnmf

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

Health

CRAN checks

13OK

Slowest check: 1.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.02

17.1%

Coverage · measured lines

100%

Documentation · exports

8

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

Documentation

READMEYes · 565 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

2.6K

CRAN downloads in the past year

Rank #17,529 · ~7/day · ~214/mo

Releases R versions

Daily download trend is not available in this view yet.

14230 days

63490 days

2.6K1 year

Compare downloads with other packages →

Also on87 r2u25 autocran

Repository

GitHub ↗ kharchenkolab/vrnmf

18Stars

4Forks

0Open issues

0Open PRs

4Releases

117Commits

4Contributors

117 commits · Last activity 2022-04-14 · 0% stars, 30d

Stars over time

2022-07-09 · 172026-07-07 · 18

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/kharchenkolab/vrnmf on 2026-08-23.

Continuous integration (2)

Travis CICircleCI

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.1

Imports (8)

graphicsica lpSolveAPIMatrixnnlsparallelquadprogstats

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Evan Biederstedt

Maintainer, Author

Authors (4)

Evan Biederstedt

Maintainer, Author

Peter Kharchenko

Author

Viktor Petukhov

Author · added in 1.0.1

Ruslan Soldatov

Author

Package Timeline

3 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
1.0.2Latest
2022-02-25 · current release · diff ↗
1.0.1
2022-01-14 · diff ↗
1.0.0
2021-08-20
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-08-20
Total releases: 3 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.1
Download size: 20 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("vrnmf")

Format

Biederstedt, E., Kharchenko, P., Petukhov, V., & Soldatov, R. (2022). vrnmf: Volume-Regularized Structured Matrix Factorization (Version 1.0.2) [Computer software]. https://doi.org/10.32614/CRAN.package.vrnmf

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 vrnmf version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-08-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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