MicrobiomeBenchmarkData
Bioc currentDatasets for benchmarking in microbiome research
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
7 3 exported
Complexity
2.9 avg / 7 max
Call network
7 nodes / 4 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
869
Files
31
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
3
Internal functions
4
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.07
testthat edition
3
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
4.2
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2022-11-01
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 9 (4 internal)includes a package overview page
- Examples that run
- 100%3 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
4 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/waldronlab/microbiomebenchmarkdata on 2026-10-18.
GitHub Pages site last deployed 2023-04-28 · The repository has a site deploy workflow
pkgdown site last built 2023-04-28
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| datasets | data.frame | 6 × 5 | No other package |
| metadata | data.frame | 17 × 16 | No other package |
| sampleMetadata | spec_tbl_df | 1,125 × 35 | No other package |
1 internal object is bundled for the package's own use and not listed here.
Topics
Suggested by (1)
People
- Samuel Gamboa author maintainer
- Marcel Ramos contributor
- Levi Waldron author
Cite
Cite this package
Run in R for the authors' entry:
citation("MicrobiomeBenchmarkData")The package provides a citation file, so citation() returns the authors' own entry.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.