"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 \insertCiteKearney2002Rogue. Consensus trees that omit rogue taxa can be more informative.
"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) \insertCiteSmithConsRogue is implemented using a quick heuristic that drops the least "stable" leaves one at a time, using an ad hoc definition of stability \insertCiteSmithConsRogue; and by a more exhaustive (and time-consuming) approach that considers dropping all possible sets of up to n leaves \insertCiteAberer2013Rogue.
The latter heuristic is implemented for the relative bipartition "information" content and Pattengale's criterion via RogueNaRok \insertCiteAberer2013Rogue.
If you find this package useful in your work, Please consider citing Smith (2021).
To cite the underlying methods, please cite \insertCiteAberer2013;textualRogue ('RogueNaRok') or \insertCiteSmithCons;textualRogue (SPIC, SCIC), as appropriate.
Andre J. Aberer email@example.com [copyright holder]
Report bugs at https://github.com/ms609/Rogue/issues/
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