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.
None published for Bioconductor
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
1,465
Files
36
Compiled share
33.3%
Has compiled src
Yes
Language breakdown
API
Exported functions
1
Internal functions
6
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
–
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
- Help pages
- 6
- 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%
- ADAPT Tutorial HTML
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| ecc_plaque | – | – | – |
| ecc_saliva | – | – | – |
3 internal objects are bundled for the package's own use and not listed here.
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' entry:
citation("ADAPT")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1101/2024.05.14.594186.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.