ADAPT
Bioc currentAnalysis of Microbiome Differential Abundance by Pooling Tobit Models
Release Lineage
Entered 3.20 · Oct 30, 2024
Current · Requires R 4.6
Description
ADAPT carries out differential abundance analysis for microbiome metagenomics data in phyloseq format. It has two innovations. One is to treat zero counts as left censored and use Tobit models for log count ratios. The other is an innovative way to find non-differentially abundant taxa as reference, then use the reference taxa to find the differentially abundant ones.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
33 1 exported
Complexity
4 avg / 11 max
Call network
33 nodes / 10 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
1,467
Files
38
Compiled share
33.3%
Has compiled src
Yes
Language breakdown
API
Exported functions
1
Internal functions
6
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.07
testthat edition
3
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
75%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
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
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Mukai Wang author maintainer
- Simon Fontaine contributor
- Hui Jiang contributor
- Gen Li author contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("ADAPT")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 v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.