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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 [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 |
Reference manual: | Rogue.pdf |
Vignettes: |
Detecting rogue taxa in Bayesian posterior tree sets |
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 imports: | TreeSearch |
Reverse suggests: | TreeDist |
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.