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 |
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 (source, R code) |
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-devel (arm64): Rogue_2.1.6.tgz, r-release (arm64): Rogue_2.1.6.tgz, r-oldrel (arm64): Rogue_2.1.6.tgz, r-devel (x86_64): 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 |
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