Package: Quartet
Version: 1.4.0
Title: Comparison of Phylogenetic Trees Using Quartet and Split
        Measures
Description: Calculates the number of four-taxon subtrees consistent
        with a pair of cladograms, calculating the symmetric quartet
        distance of Bandelt & Dress (1986), Reconstructing the shape of
        a tree from observed dissimilarity data, Advances in Applied
        Mathematics <doi:10.1016/0196-8858(86)90038-2>, using the
        tqDist algorithm of Sand et al. (2014), tqDist: a library for
        computing the quartet and triplet distances between binary or
        general trees, Bioinformatics
        <doi:10.1093/bioinformatics/btu157> for pairs of binary trees;
        calculating the rooted triplet distance using the CPDT
        algorithm of Jansson & Rajaby (2017), A more practical
        algorithm for the rooted triplet distance, Journal of
        Computational Biology <doi:10.1089/cmb.2016.0185>; these
        distances can be used to construct consensus trees via the
        greedy heuristic of Takazawa et al. (2026), Outperforming the
        majority-rule consensus tree using fine-grained dissimilarity
        measures, bioRxiv <doi:10.64898/2026.03.16.712085>.
URL: https://ms609.github.io/Quartet/,
        https://github.com/ms609/Quartet/
BugReports: https://github.com/ms609/Quartet/issues/
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("Jesper", "Jansson",
                      email = "jj@i.kyoto-u.ac.jp",
                      comment = c(ORCID = "0000-0001-6859-8932"),
                      role = c("ctb", "cph")),
               person("Ramesh", "Rajaby", role = c("ctb", "cph")),
               person("Andreas", "Sand", role = c("ctb", "cph")),
               person("Gerth", "Stølting Brodal", role = c("ctb", "cph")),
               person("Rolf", "Fagerberg", role = c("ctb", "cph")),
               person("Thomas", "Mailund", role = c("ctb", "cph")),
               person("Christian N. S.", "Pedersen",
                      email = "cstorm@birc.au.dk",
                      comment = c(ORCID = "0000-0002-8947-6771"),
                      role = c("ctb", "cph")),
               person("Jens", "Johansen", role = c("ctb", "cph")),
               person("Morten K.", "Holt", role = c("ctb", "cph"))
            )
Copyright: Incorporates code modified from tqDist
        <doi:10.1093/bioinformatics/btu157> and from CPDT-dist
        <doi:10.1089/cmb.2016.0185>.
License: GPL (>= 2)
Encoding: UTF-8
Language: en-GB
Depends: R (>= 3.6.0), TreeTools (>= 1.4.0),
Imports: ape, PlotTools, Rdpack (>= 0.7), Ternary (>= 1.0),
Suggests: bookdown, knitr, phangorn, rmarkdown, testthat, TreeDist,
        usethis, vdiffr,
Config/Needs/check: rcmdcheck, tinytex,
Config/Needs/coverage: covr
Config/Needs/memcheck: devtools
Config/Needs/metadata: codemetar
Config/Needs/revdeps: revdepcheck
Config/Needs/website: pkgdown
Config/roxygen2/version: 8.0.0
RdMacros: Rdpack
LinkingTo: Rcpp, TreeTools,
LazyData: true
ByteCompile: true
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Config/pak/sysreqs: cmake make libuv1-dev zlib1g-dev
Repository: https://phylotastic.r-universe.dev
Date/Publication: 2026-06-19 20:46:57 UTC
RemoteUrl: https://github.com/ms609/Quartet
RemoteRef: HEAD
RemoteSha: 638f980dc31c845d26dbf0247261291a1ff50dde
NeedsCompilation: yes
Packaged: 2026-06-23 23:43:48 UTC; root
Author: Martin R. Smith [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0001-5660-1727>),
  Jesper Jansson [ctb, cph] (ORCID:
    <https://orcid.org/0000-0001-6859-8932>),
  Ramesh Rajaby [ctb, cph],
  Andreas Sand [ctb, cph],
  Gerth Stølting Brodal [ctb, cph],
  Rolf Fagerberg [ctb, cph],
  Thomas Mailund [ctb, cph],
  Christian N. S. Pedersen [ctb, cph] (ORCID:
    <https://orcid.org/0000-0002-8947-6771>),
  Jens Johansen [ctb, cph],
  Morten K. Holt [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>