DESCRIPTION

Package: Rogue
Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
Version: 2.1.6
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 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: 7.3.1
Roxygen: list(markdown = TRUE)