rogue

Identify rogue taxa in phylogenetic trees within R

https://github.com/ms609/rogue

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 12 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
✓
Committers with academic emails
2 of 5 committers (40.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (16.1%) to scientific vocabulary

Keywords

consensus-tree phylogenetic-trees phylogenetics r-package

Last synced: 6 months ago · JSON representation

Repository

Identify rogue taxa in phylogenetic trees within R

Basic Info

Host: GitHub
Owner: ms609
Language: Bluespec
Default Branch: main
Homepage: https://ms609.github.io/Rogue
Size: 10.3 MB

Statistics

Stars: 3
Watchers: 3
Forks: 0
Open Issues: 11
Releases: 10

Topics

consensus-tree phylogenetic-trees phylogenetics r-package

Created over 4 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing Code of conduct Codemeta

Rogue

"Rogue" implements approaches to identify rogue taxa in phylogenetic analysis. Rogues are wildcard leaves whose uncertain position reduces the resolution of consensus trees. Consensus trees that omit rogue taxa can be more informative.

"Rogue" allows the user to select a concept of "information" by which the quality of consensus trees should be evaluated, and a heuristic approach by which rogue taxa should be identified.

Rogue detection using the phylogenetic and clustering information content measures (Smith, 2022) is implemented using a quick heuristic that drops the least "stable" leaves one at a time, using an ad hoc definition of stability (Smith, 2022); and by a more exhaustive (and time-consuming) approach that considers dropping all possible sets of up to n leaves (Aberer et al. 2013).

The latter heuristic is implemented for the relative bipartition "information" content and Pattengale's criterion via RogueNaRok (Aberer et al. 2013).

Installation

Install and load the stable version from CRAN as normal: r install.packages("Rogue") library("Rogue")

Alternatively, install the development version from GitHub with r devtools::install_github("ms609/Rogue", args = "--recursive") (Requires git to be installed and added to your PATH system environment variable; you may also require the "curl" R package.)

Citing 'Rogue'

If you find this package useful in your work, please consider citing Smith (2021).

To cite the underlying methods, please cite Aberer et al. (2013) ('RogueNaRok') or Smith (2022), as appropriate.

References

A.J. Aberer, D. Krompass, A. Stamatakis (2013): Pruning rogue taxa improves phylogenetic accuracy: an efficient algorithm and webservice. Systematic Biology 62(1): 162-166, doi:10.1093/sysbio/sys078.

M.R. Smith (2021): Rogue: Identify rogue taxa in sets of phylogenetic trees. Zenodo, doi:10.5281/zenodo.5037327.

M.R. Smith (2022): Using information theory to detect rogue taxa and improve consensus trees. Systematic Biology 71(5): 986–1008, doi:10.1093/sysbio/syab099

Owner

Name: Martin R. Smith
Login: ms609
Kind: user
Location: Durham, UK
Company: Department of Earth Sciences, Durham University

Website: https://orcid.org/0000-0001-5660-1727
Twitter: PalaeoSmith
Repositories: 21
Profile: https://github.com/ms609

Palaeontology & phylogenetics

CodeMeta (codemeta.json)

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  "description": "Rogue (\"wildcard\") taxa are leaves with uncertain phylogenetic position. Their position may vary from tree to tree under inference methods that yield a tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony). The presence of rogue taxa in a tree set can potentially remove all information from a consensus tree. The information content of a consensus tree - a function of its resolution and branch support values - can often be increased by removing rogue taxa. 'Rogue' provides an explicitly information-theoretic approach to rogue detection (Smith 2022) <doi:10.1093/sysbio/syab099>, and an interface to 'RogueNaRok' (Aberer et al. 2013) <doi:10.1093/sysbio/sys078>.",
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GitHub Events

Total

Issues event: 5
Watch event: 1
Delete event: 2
Issue comment event: 6
Push event: 32
Pull request event: 5
Create event: 3

Last Year

Issues event: 5
Watch event: 1
Delete event: 2
Issue comment event: 6
Push event: 32
Pull request event: 5
Create event: 3

Committers

Last synced: over 2 years ago

All Time

Total Commits: 211
Total Committers: 5
Avg Commits per committer: 42.2
Development Distribution Score (DDS): 0.441

Past Year

Commits: 10
Committers: 2
Avg Commits per committer: 5.0
Development Distribution Score (DDS): 0.2

Top Committers

Name	Email	Commits
Martin Smith	m**s@g**m	118
Martin R. Smith	1****9	62
Martin R. Smith	m**h@d**k	14
GitHub Actions	a**s@g**m	9
SMITH	p**8@d**k	8

Committer Domains (Top 20 + Academic)

durham.ac.uk: 2 github.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 16
Total pull requests: 16
Average time to close issues: 4 months
Average time to close pull requests: 2 days
Total issue authors: 2
Total pull request authors: 1
Average comments per issue: 0.5
Average comments per pull request: 0.63
Merged pull requests: 14
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 2
Pull requests: 2
Average time to close issues: 32 minutes
Average time to close pull requests: about 2 hours
Issue authors: 2
Pull request authors: 1
Average comments per issue: 2.0
Average comments per pull request: 0.0
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

ms609 (15)
HS6986 (1)

Pull Request Authors

ms609 (19)
Copilot (1)

Top Labels

Issue Labels

enhancement (1) optimization (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 959 last-month

Total dependent packages: 2
Total dependent repositories: 3
Total versions: 10
Total maintainers: 1

cran.r-project.org: Rogue

Identify Rogue Taxa in Sets of Phylogenetic Trees

Homepage: https://github.com/ms609/Rogue/
Documentation: http://cran.r-project.org/web/packages/Rogue/Rogue.pdf
License: GPL (≥ 3)
Latest release: 2.1.7
published 8 months ago

Versions: 10
Dependent Packages: 2
Dependent Repositories: 3
Downloads: 959 Last month

Rankings

Dependent packages count: 13.7%

Dependent repos count: 16.5%

Average: 23.4%

Forks count: 27.8%

Stargazers count: 27.8%

Downloads: 31.3%

Maintainers (1)

martin.smith@durham.ac.uk

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

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matrixStats * imports
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utils * imports
knitr * suggests
rmarkdown * suggests
spelling * suggests
testthat * suggests

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rogue

Science Score: 59.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Rogue

Installation

Citing 'Rogue'

References

Owner

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

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All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

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cran.r-project.org: Rogue

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Maintainers (1)

Dependencies