R Observatory: Metrics for MetMashR version 1.6.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MetMashR

Bioc current

Metabolite Mashing with R

v1.6.0 · software · GPL-3

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.20 · Oct 30, 2024

Current · Requires R 4.6

1.0 In 4 of 49 releases 3.23

Description

A package to merge, filter sort, organise and otherwise mash together metabolite annotation tables. Metabolite annotations can be imported from multiple sources (software) and combined using workflow steps based on S4 class templates derived from the `struct` package. Other modular workflow steps such as filtering, merging, splitting, normalisation and rest-api queries are included.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

116 91 exported

Complexity

2 avg / 8 max

Call network

116 nodes / 5 edges

Test coverage is not measured for Bioconductor packages; 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.

Code

Structure

Lines of code

23,426

Files

254

Compiled share

0%

Has compiled src

No

Language breakdown

R 11,530 (49.2%)Tests 3,299 (14.1%)Docs 6,029 (25.7%)Vignettes 2,568 (11%)

API

Exported functions

94

Internal functions

25

Recent export changes

v3.22+4 upset_intersections, upset_max_groups, upset_min_groups +1 more −1 openbabel_structure

v3.20+91 AnnotationDb_database, AnnotationDb_select, BiocFileCache_database +88 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.29

testthat edition

3

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

0

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.3.0

System requirements

–

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

4

First release

2024-10-29

Latest release

2026-04-28

Avg cadence

181 days

Cold removal rate

100%

Dep drift

1

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 70 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 99%
Documented parameters: 98%
Return-value docs: 100%
References docs: 45%

Topics

Software › WorkflowStep

Software › ResearchField › Metabolomics

Software › WorkflowStep › Pathways › KEGG

People

Gavin Rhys Lloyd author maintainer
Ralf Johannes Maria Weber author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MetMashR")

Format

Lloyd, G. R., & Weber, R. J. M. (2026). MetMashR: Metabolite Mashing with R (Version 1.6.0) [Computer software]. https://bioconductor.org/packages/MetMashR

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 MetMashR version 1.6.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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