simona
Bioc currentSemantic Similarity on Bio-Ontologies
Release Lineage
Entered 3.18 · Oct 25, 2023
Current · Requires R 4.6
Description
This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
519 89 exported
Complexity
3.3 avg / 60 max
Call network
519 nodes / 756 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
24,144
Files
361
Compiled share
21.4%
Has compiled src
Yes
Language breakdown
API
Exported functions
91
Internal functions
228
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.13
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
25%
Unsafe pattern score
0
Dep constraint coverage
5.9%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
2
C++ standard
C++11
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
6
First release
2024-02-05
Latest release
2026-04-28
Avg cadence
168 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
- 94%
- References docs
- 0%
Topics
Depended on by (2)
Bioconductor (2)
People
- Zuguang Gu author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("simona")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.