Package: Rogue
Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
Version: 2.0.0
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")
            )
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, forthcoming), 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 (>= 2.1.1), TreeTools
        (>= 1.5.0), utils,
Suggests: 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
RoxygenNote: 7.1.1
NeedsCompilation: yes
Packaged: 2021-09-13 09:12:58 UTC; ms609
Author: Martin R. Smith [aut, cre, cph]
    (<https://orcid.org/0000-0001-5660-1727>),
  Andre J. Aberer [aut, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Repository: CRAN
Date/Publication: 2021-09-13 15:30:21 UTC
