R Observatory: Metrics for mums2 version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

mums2

0.1.1

Microbial Ecology by Tandem Mass Spectrometry

0packages depend

764downloads / year

85.5%test coverage

13/13checks pass

Overview

About

Maintained by Patrick SchlossFirst published 2026-06-102 releasesCRAN page ↗GitHub ↗

Tools that researchers can use to analyze untargeted metabolomics data generated using tandem mass spectroscopy from microbial communities. The overall approach taken to analyze metabolomics data parallels that used to analyze microbial communities using 16S rRNA gene sequencing data. Thus, we have a number of methods a user is able to use to generate data. Firstly, users can import Mass Spectrometry 1(MS1) data and filter it. Users are then able to match Mass Spectrometry 2(MS2) data to the filtered (or unfiltered) MS1 data. With the matched data users are able to cluster it, annotate it, predict de novo chemical formulas and calculate alpha and beta diversity. For chemical formula predictions, this was the method used; "Towards de novo identification of metabolites by analyzing tandem mass spectra" (Sebastian Böcker, Florian Rasche (2008) doi:10.1093/bioinformatics/btn270). The similarity/dissimilarity calculations we used to cluster our data together was: "Spectral entropy outperforms MS/MS dot product similarity for small-molecule compound identification" (Li, Y., Kind, T., Folz, J. et al. (2021) doi:10.1038/s41592-021-01331-z) and "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking" (Wang, M., Carver, J., Phelan, V. et al. (2021) doi:10.1038/nbt.3597).

Install

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

install.packages("mums2", 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("mums2/mums2")

Development version from mums2/mums2. 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-mums2

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-mums2

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-mums2

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

Health

CRAN checks

13OK

Slowest check: 20.0 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 82.04

85.5%

Coverage · measured lines

100%

Documentation · exports

9

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
OK2026-06-26
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-11
5 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE

Documentation

READMEYes · 168 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 97%
References docs: 11%

Downloads

764

CRAN downloads in the past year

Rank #13,197 · ~2/day · ~64/mo

Releases R versions

Daily download trend is not available in this view yet.

24630 days

76490 days

7641 year

Compare downloads with other packages →

Also on52 r2u5 autocran

Repository

GitHub ↗ mums2/mums2

1Stars

0Forks

0Open issues

0Open PRs

1Releases

77Commits

3Contributors

License GPL-3.0 · 77 commits · Last activity 2026-08-17 · 0% stars, 30d

Stars over time

2026-06-03 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/mums2/mums2 on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (2)

lintrRStudio project

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (9)

clustur Rcpp data.table mpactrutilsstatsparallelxml2 RaMS

LinkingTo (5)

sitmo Rcpp RcppThread testthat RcppProgress

Suggests (5)

knitr rmarkdown testthat tidyverse networkD3

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (8)

Maintainer (1)

Patrick Schloss

Author, Maintainer

Authors (3)

Patrick Schloss

Author, Maintainer

Gregory Johnson

Author

Allison Mason

Author

Contributors (5)

Yuanyue Li

Contributor, Copyright holder

Marcel Martin

Contributor, Copyright holder

Anton Pervukhin

Contributor, Copyright holder

Florian Rasche

Contributor, Copyright holder

Henner Sudek

Contributor, Copyright holder

Copyright holders (5)

Yuanyue Li

Contributor, Copyright holder

Marcel Martin

Contributor, Copyright holder

Anton Pervukhin

Contributor, Copyright holder

Florian Rasche

Contributor, Copyright holder

Henner Sudek

Contributor, Copyright holder

Package Timeline

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

0.1.1Latest
2026-06-25 · current release · diff ↗
0.1.0
2026-06-10
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-10
Total releases: 2 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Download size: 7.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("mums2")

Format

Schloss, P., Johnson, G., Li, Y., Martin, M., Mason, A., Pervukhin, A., Rasche, F., & Sudek, H. (2026). mums2: Microbial Ecology by Tandem Mass Spectrometry (Version 0.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.mums2

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 mums2 version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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