Package: Rogue
Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
Version: 2.2.0
Authors@R: c(
  person("Martin R.", 'Smith',
         email = "martin.smith@durham.ac.uk", 
         role = c("aut", "cre", "cph"),
         comment = c(ORCID = "0000-0001-5660-1727")),
  person(given = "Andre J.", family="Aberer",
         role = c("aut", "cph"),
         email = "andre.aberer@googlemail.com",
         comment = "RogueNaRok"
         )
  )
License: GPL (>= 3)
Description: 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>.
URL: https://github.com/ms609/Rogue/,
        https://github.com/aberer/RogueNaRok/,
        https://github.com/ms609/RogueNaRok/
BugReports: https://github.com/ms609/Rogue/issues/
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
        (>= 1.9.1.9003), utils,
Suggests: knitr, PlotTools, rmarkdown, spelling, testthat,
Config/Needs/github-actions: callr, pkgbuild, rcmdcheck,
Config/Needs/coverage: covr
Config/Needs/memcheck: devtools
Config/Needs/metadata: codemetar
Config/Needs/website: pkgdown
RdMacros: Rdpack
SystemRequirements: C99
ByteCompile: true
Encoding: UTF-8
Language: en-GB
VignetteBuilder: knitr
RoxygenNote: 7.3.3
NeedsCompilation: yes
Packaged: 2026-03-25 09:36:59 UTC; pjjg18
Author: Martin R. Smith [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0001-5660-1727>),
  Andre J. Aberer [aut, cph] (RogueNaRok)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Repository: CRAN
Date/Publication: 2026-03-25 10:40:02 UTC
Built: R 4.6.0; x86_64-apple-darwin20; 2026-04-25 20:52:24 UTC; unix
Archs: Rogue.so.dSYM
