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: |
2.1.1 |
| 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: |
2022-07-20 |
| 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 |
| CRAN checks: |
Rogue results |
Documentation:
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