Package: Rogue
Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
Version: 2.2.1.9000
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 tips.
        'Rogue' provides an explicitly information-theoretic approach
        to rogue detection (Smith 2022) <doi:10.1093/sysbio/syab099>,
        an interface to 'RogueNaRok' (Aberer et al. 2013)
        <doi:10.1093/sysbio/sys078>, and heuristics for measuring leaf
        instability.
URL: https://ms609.github.io/Rogue/
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), 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
Config/roxygen2/version: 8.0.0
RdMacros: Rdpack
SystemRequirements: C++17
ByteCompile: true
Encoding: UTF-8
Language: en-GB
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Config/pak/sysreqs: cmake make libuv1-dev zlib1g-dev
Repository: https://phylotastic.r-universe.dev
Date/Publication: 2026-06-29 08:52:46 UTC
RemoteUrl: https://github.com/ms609/Rogue
RemoteRef: HEAD
RemoteSha: 573cf9b63ffd0fb9be61f898e9073eef6ac0c200
NeedsCompilation: yes
Packaged: 2026-06-29 10:44:10 UTC; root
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>