"Rogue" implements approaches to identify rogue taxa in phylogenetic analysis. Rogues are wildcard leaves whose uncertain position, perhaps a result of missing or conflicting data, reduces the resolution of consensus trees Kearney2002Rogue. Consensus trees that omit rogue taxa can be more informative.
Maintainer: Martin R. Smith martin.smith@durham.ac.uk (ORCID) [copyright holder]
Authors:
Andre J. Aberer andre.aberer@googlemail.com [copyright holder]
"Rogue" allows the user to select a concept of "information" by which the quality of consensus trees should be evaluated, and a heuristic approach by which rogue taxa should be identified.
Rogue detection using the phylogenetic and clustering information content measures (SPIC, SCIC) SmithConsRogue is implemented using a quick heuristic that drops the least "stable" leaves one at a time, using an ad hoc definition of stability SmithConsRogue; and by a more exhaustive (and time-consuming) approach that considers dropping all possible sets of up to n leaves Aberer2013Rogue.
The latter heuristic is implemented for the relative bipartition "information" content and Pattengale's criterion via RogueNaRok Aberer2013Rogue.
If you find this package useful in your work, Please consider citing Smith (2021).
To cite the underlying methods, please cite Aberer2013;textualRogue ("RogueNaRok") or SmithCons;textualRogue (SPIC, SCIC), as appropriate.