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DESCRIPTION
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DESCRIPTION
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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: 7.2.3
NeedsCompilation: yes
Packaged: 2023-11-29 09:49:02 UTC; pjjg18
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: 2023-11-29 11:10:02 UTC