Package: Rogue 2.1.6
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:
Rogue_2.1.6.tar.gz
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Rogue.pdf |Rogue.html✨
Rogue/json (API)
NEWS
# Install 'Rogue' in R: |
install.packages('Rogue', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ms609/rogue/issues
consensus-treephylogenetic-treesphylogenetics
Last updated 7 months agofrom:7c2e98ff02. Checks:OK: 9. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 21 2024 |
R-4.5-win-x86_64 | OK | Aug 21 2024 |
R-4.5-linux-x86_64 | OK | Aug 21 2024 |
R-4.4-win-x86_64 | OK | Aug 21 2024 |
R-4.4-mac-x86_64 | OK | Aug 21 2024 |
R-4.4-mac-aarch64 | OK | Aug 21 2024 |
R-4.3-win-x86_64 | OK | Aug 21 2024 |
R-4.3-mac-x86_64 | OK | Aug 21 2024 |
R-4.3-mac-aarch64 | OK | Aug 21 2024 |
Exports:C_RogueNaRokColByStabilityCopheneticGraphGeodesicQuickRogueRogueTaxaTipInstabilityTipVolatility
Dependencies:apebase64encbitbit64bitopsbslibcachemclicolorspacecommonmarkcrayondigestfastmapfastmatchfontawesomefsgluehtmltoolshttpuvjquerylibjsonlitelaterlatticelifecyclemagrittrmatrixStatsmemoisemimenlmePlotToolspromisesR.cacheR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRcppRcppArmadilloRcppGSLRcppParallelRcppZigguratRCurlRdpackRfastrlangsassshinyshinyjssourcetoolsTreeDistTreeToolswithrxtable
Readme and manuals
Help Manual
Help page | Topics |
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Drop rogue taxa to generate a more informative consensus | C_RogueNaRok QuickRogue RogueTaxa |
Tip instability | ColByStability TipInstability |
Detect rogue taxa using phylogenetic information distance | TipVolatility |