miaSim
Bioc currentMicrobiome Data Simulation
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell's Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to (Tree)SummarizedExperiment objects.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
22 13 exported
Complexity
7.7 avg / 24 max
Call network
22 nodes / 25 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
4,205
Files
61
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
13
Internal functions
9
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.09
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
Artistic-2.0 | file LICENSE
License flags
SPDX valid, not OSI
History
Versions
10
First release
2021-10-26
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
5
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 18 (1 internal)
- Examples that run
- 100%13 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 22%
- miaSim HTML
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/microbiome/miasim on 2026-10-18.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Topics
People
- Yagmur Simsek maintainer author
- Tuomas Borman author
- Karoline Faust author
- Yu Gao author
- Daniel Rios Garza author
- Emma Gheysen author
- Akewak Jeba contributor
- Leo Lahti author
- Geraldson Muluh contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("miaSim")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 v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.