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Bioc current

Visualization of Phylogenetic Networks

v1.18.0 · software · Artistic-2.0
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Release Lineage

Entered 3.14 · Oct 27, 2021

Current · Requires R 4.6

1.0 In 10 of 49 releases 3.23

Description

Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending. 'ggtree' and using functions from 'ape' and 'phangorn'. It extends the 'ggtree' package [@Yu2017] to allow the visualization of phylogenetic networks using the 'ggplot2' syntax. It offers an alternative to the plot functions already available in 'ape' Paradis and Schliep (2019) <doi:10.1093/bioinformatics/bty633> and 'phangorn' Schliep (2011) <doi:10.1093/bioinformatics/btq706>.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

8 6 exported

Complexity

4.8 avg / 7 max

Call network

8 nodes / 3 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →
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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

1,442

Files

30

Compiled share

0%

Has compiled src

No

Language breakdown

R 428 (29.7%)Tests 3 (0.2%)Docs 308 (21.4%)Vignettes 703 (48.8%)

API

Exported functions

6

Internal functions

2

Recent export changes

v3.22+1 swap_hybrid_minor

Testing & CI

Has tests

Yes

Test-to-code ratio

0.01

testthat edition

–

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

37.5%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.1

System requirements

–

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

10

First release

2021-10-26

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

–

Dep drift

2

LOC over versions

v3.14: 1,075 LOCv3.15: 1,261 LOCv3.16: 1,261 LOCv3.17: 1,261 LOCv3.18: 1,261 LOCv3.19: 1,261 LOCv3.20: 1,261 LOCv3.21: 1,261 LOCv3.22: 1,442 LOCv3.23: 1,442 LOC

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

Documentation
READMEYes · 170 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 0% structuredCode of conductNoContributing guideNo
Examples that run
100%
Documented parameters
100%
Return-value docs
100%
References docs
14%

Topics

Software
Software › WorkflowStep › Visualization
Software › ResearchField › Phylogenetics
Software › WorkflowStep › Alignment
Software › StatisticalMethod › Clustering
Software › WorkflowStep › Alignment › MultipleSequenceAlignment
Software › Infrastructure › DataImport

People

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