RCM
Bioc currentFit row-column association models with the negative binomial distribution for the microbiome
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
Combine ideas of log-linear analysis of contingency table, flexible response function estimation and empirical Bayes dispersion estimation for explorative visualization of microbiome datasets. The package includes unconstrained as well as constrained analysis. In addition, diagnostic plot to detect lack of fit are available.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
69 10 exported
Complexity
5.7 avg / 87 max
Call network
69 nodes / 88 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
8,389
Files
157
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
12
Internal functions
59
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.04
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
100%
Unsafe pattern score
0
Dep constraint coverage
6.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
–
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
15
First release
2019-05-02
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
3
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 70
- Examples that run
- 100%12 run in a plain check
- Exported functions with examples
- 92%
- Documented parameters
- 92%
- Return-value docs
- 100%
- Help pages citing references
- 0% with a bibliography file
Repository practices
4 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/centerforstatistics-ugent/rcm on 2026-10-22.
GitHub Pages site last deployed 2026-07-17
Datasets
Topics
People
- Stijn Hawinkel maintainer author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("RCM")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.