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: 2.1.3
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 (≥ 1.6.0.9007), utils
Suggests: knitr, rmarkdown, spelling, testthat
Published: 2022-09-26
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_2.1.3.tar.gz
Windows binaries: r-devel: Rogue_2.1.3.zip, r-release: Rogue_2.1.3.zip, r-oldrel: Rogue_2.1.3.zip
macOS binaries: r-release (arm64): Rogue_2.1.3.tgz, r-oldrel (arm64): Rogue_2.1.3.tgz, r-release (x86_64): Rogue_2.1.3.tgz, r-oldrel (x86_64): Rogue_2.1.3.tgz
Old sources: Rogue archive

Reverse dependencies:

Reverse imports: TreeSearch
Reverse suggests: TreeDist

Linking:

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