doi:10.1093/sysbio/syab099>, and an interface to 'RogueNaRok' (Aberer et al. 2013) <doi:10.1093/sysbio/sys078>.">

Rogue: Identify Rogue Taxa in Sets of Phylogenetic Trees (original) (raw)

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: 2.1.7
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: 2025-07-01
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

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