mia
Bioc currentMicrobiome analysis
Release Lineage
Entered 3.13 · May 20, 2021
Current · Requires R 4.6
Description
mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
385 38 exported
Complexity
4.2 avg / 46 max
Call network
385 nodes / 340 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
34,859
Files
201
Compiled share
3%
Has compiled src
Yes
Language breakdown
API
Exported functions
175
Internal functions
300
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.29
testthat edition
–
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
3.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0
System requirements
–
C++ standard
–
License
Artistic-2.0 | file LICENSE
License flags
SPDX valid, not OSI
History
Versions
11
First release
2021-07-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
11
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 95%
- Documented parameters
- 93%
- Return-value docs
- 97%
- References docs
- 40%
Topics
Depended on by (22)
Bioconductor (21)
CRAN (1)
People
- Tuomas Borman author maintainer
- Eineje Ameh contributor
- Moritz Emanuel Beber contributor
- Aituar Bektanov contributor
- Chouaib Benchraka contributor
- Giulio Benedetti contributor
- Domenick Braccia contributor
- Danielle Callan contributor
- Yang Cao contributor
- Héctor Corrada Bravo contributor
- Basil Courbayre contributor
- Noah De Gunst contributor
- Pande Erawijantari contributor
- Felix G.M. Ernst author
- Sam Hillman contributor
- Rasmus Hindström contributor
- Shadman Ishraq contributor
- Akewak Jeba contributor
- Jayaram Kancherla contributor
- Leo Lahti author
- Himmi Lindgren contributor
- Geraldson Muluh contributor
- Nathan D. Olson contributor
- Hervé Pagès contributor
- Jesse Pasanen contributor
- Théotime Pralas contributor
- Katariina Pärnänen contributor
- Marcel Ramos contributor
- Artur Sannikov contributor
- Sudarshan A. Shetty author
- Rajesh Shigdel contributor
- Eetu Tammi contributor
- Levi Waldron contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("mia")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.
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.