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 [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: | Paleontology,Phylogenetics |
| CRAN checks: | Rogue results |