Package: Rogue 2.1.6

Martin R. Smith

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>.

Authors:Martin R. Smith [aut, cre, cph], Andre J. Aberer [aut, cph]

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Bug tracker:https://github.com/ms609/rogue/issues

On CRAN:

consensus-treephylogenetic-treesphylogenetics

8 exports 2 stars 1.60 score 55 dependencies 2 dependents 56 scripts 433 downloads

Last updated 7 months agofrom:7c2e98ff02. Checks:OK: 9. Indexed: no.

Exports:C_RogueNaRokColByStabilityCopheneticGraphGeodesicQuickRogueRogueTaxaTipInstabilityTipVolatility

Dependencies:apebase64encbitbit64bitopsbslibcachemclicolorspacecommonmarkcrayondigestfastmapfastmatchfontawesomefsgluehtmltoolshttpuvjquerylibjsonlitelaterlatticelifecyclemagrittrmatrixStatsmemoisemimenlmePlotToolspromisesR.cacheR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRcppRcppArmadilloRcppGSLRcppParallelRcppZigguratRCurlRdpackRfastrlangsassshinyshinyjssourcetoolsTreeDistTreeToolswithrxtable