philr
Bioc currentPhylogenetic partitioning based ILR transform for metagenomics data
Release Lineage
Entered 3.4 · Oct 18, 2016
Current · Requires R 4.6
Description
PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
38 19 exported
Complexity
2.9 avg / 26 max
Call network
38 nodes / 45 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
2,923
Files
49
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
19
Internal functions
19
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.16
testthat edition
–
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
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
20
First release
2016-10-17
Latest release
2026-04-28
Avg cadence
183 days
Cold removal rate
–
Dep drift
1
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
- 41%
Topics
Depended on by (3)
People
- Justin Silverman author maintainer
- Leo Lahti contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("philr")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.