sitePath
Bioc currentPhylogeny-based sequence clustering with site polymorphism
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
Using site polymorphism is one of the ways to cluster DNA/protein sequences but it is possible for the sequences with the same polymorphism on a single site to be genetically distant. This package is aimed at clustering sequences using site polymorphism and their corresponding phylogenetic trees. By considering their location on the tree, only the structurally adjacent sequences will be clustered. However, the adjacent sequences may not necessarily have the same polymorphism. So a branch-and-bound like algorithm is used to minimize the entropy representing the purity of site polymorphism of each cluster.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
244 21 exported
Complexity
3 avg / 24 max
Call network
244 nodes / 162 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
9,189
Files
108
Compiled share
21.6%
Has compiled src
Yes
Language breakdown
API
Exported functions
25
Internal functions
131
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.16
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
15
First release
2019-06-25
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
9
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 29 (1 internal)
- Examples that run
- 100%21 run in a plain check
- Exported functions with examples
- 90%
- Documented parameters
- 100%
- Return-value docs
- 90%
- Help pages citing references
- 0%
Repository practices
7 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/wuaipinglab/sitepath on 2026-10-18.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2022-09-26 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| h3n2_align | alignment | 4 elements | No other package |
| h3n2_align_reduced | alignment | 4 elements | No other package |
| h3n2_tree | phylo | 5 elements | No other package |
| h3n2_tree_reduced | phylo | 4 elements | No other package |
| sars2_align | alignment | 4 elements | No other package |
| sars2_tree | phylo | 4 elements | No other package |
| zikv_align | alignment | 4 elements | No other package |
| zikv_align_reduced | alignment | 4 elements | No other package |
| zikv_tree | phylo | 4 elements | No other package |
| zikv_tree_reduced | phylo | 4 elements | No other package |
Topics
People
- Chengyang Ji author maintainer copyright holder
- Aiping Wu thesis advisor
- Hangyu Zhou thesis advisor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("sitePath")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.