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Rogue: Identify Rogue Taxa in Sets of Phylogenetic Trees

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>.

Version: 2.1.6
Depends: R (≥ 3.5.0)
Imports: ape (≥ 5.0), cli (≥ 3.0), fastmatch, grDevices, matrixStats, Rdpack (≥ 0.7), Rfast, stats, TreeDist (> 2.2.0), TreeTools (≥ 1.9.1.9003), utils
Suggests: knitr, PlotTools, rmarkdown, spelling, testthat
Published: 2023-11-29
DOI: 10.32614/CRAN.package.Rogue
Author: Martin R. Smith ORCID iD [aut, cre, cph], Andre J. Aberer [aut, cph]
Maintainer: Martin R. Smith <martin.smith at durham.ac.uk>
BugReports: https://github.com/ms609/Rogue/issues/
License: GPL (≥ 3)
URL: https://github.com/ms609/Rogue/, https://github.com/aberer/RogueNaRok/, https://github.com/ms609/RogueNaRok/
NeedsCompilation: yes
SystemRequirements: C99
Language: en-GB
Citation: Rogue citation info
Materials: NEWS
In views: Phylogenetics
CRAN checks: Rogue results

Documentation:

Reference manual: Rogue.pdf
Vignettes: Detecting rogue taxa in Bayesian posterior tree sets

Downloads:

Package source: Rogue_2.1.6.tar.gz
Windows binaries: r-devel: Rogue_2.1.6.zip, r-release: Rogue_2.1.6.zip, r-oldrel: Rogue_2.1.6.zip
macOS binaries: r-release (arm64): Rogue_2.1.6.tgz, r-oldrel (arm64): Rogue_2.1.6.tgz, r-release (x86_64): Rogue_2.1.6.tgz, r-oldrel (x86_64): Rogue_2.1.6.tgz
Old sources: Rogue archive

Reverse dependencies:

Reverse imports: TreeSearch
Reverse suggests: TreeDist

Linking:

Please use the canonical form https://CRAN.R-project.org/package=Rogue to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.