Package: TreeDist
Title: Calculate and Map Distances Between Phylogenetic Trees
Version: 2.14.1.9000
Authors@R: c(person("Martin R.", "Smith",
                    email = "martin.smith@durham.ac.uk", 
                    role = c("aut", "cre", "cph", "prg"), 
                    comment = c(ORCID = "0000-0001-5660-1727")),
             person("Roy", "Jonker", email = "roy_jonker@magiclogic.com",
                    role = c("prg", "cph"), comment = "LAP algorithm"),
             person("Yong", "Yang", email = "yongyanglink@gmail.com",
                    role = c("ctb", "cph"), comment = "LAP algorithm"),
             person("Yi", "Cao", role = c("ctb", "cph"), comment = "LAP algorithm"),
             person("Neil", "Kaye", role = c("cph"), comment = "Mercator image")
            )
License: GPL (>= 3)
Description: Implements measures of tree similarity, including
        information-based generalized Robinson-Foulds distances
        (Phylogenetic Information Distance, Clustering Information
        Distance, Matching Split Information Distance; Smith 2020)
        <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds
        distances (Bocker et al. 2013)
        <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al.
        (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching
        Split Distance (Bogdanowicz & Giaro 2012)
        <doi:10.1109/TCBB.2011.48>; the Hierarchical Mutual Information
        (Perotti et al. 2015) <doi:10.1103/PhysRevE.92.062825>; Maximum
        Agreement Subtree distances; the Kendall-Colijn (2016) distance
        <doi:10.1093/molbev/msw124>, and the Nearest Neighbour
        Interchange (NNI) distance, approximated per Li et al. (1996)
        <doi:10.1007/3-540-61332-3_168>. Includes tools for visualizing
        mappings of tree space (Smith 2022)
        <doi:10.1093/sysbio/syab100>, for identifying islands of trees
        (Silva and Wilkinson 2021) <doi:10.1093/sysbio/syab015>, for
        calculating the median of sets of trees, and for computing the
        information content of trees and splits.
Copyright: Jonker-Volgenant Linear Assignment Problem implementation by
        Roy Jonker modified by Yong Yang and Yi Cao.
URL: https://ms609.github.io/TreeDist/,
        https://github.com/ms609/TreeDist/
BugReports: https://github.com/ms609/TreeDist/issues/
Additional_repositories: https://ms609.github.io/packages/
Depends: R (>= 4.0), stats,
Imports: ape (>= 5.0), cli (>= 3.0), Rdpack (>= 0.7), shiny, shinyjs,
        TreeTools (>= 2.1.0),
Suggests: bookdown, cluster, ggplot2, hypervolume, kdensity, knitr,
        MASS, parallel, phangorn (>= 2.2.1), plotly, PlotTools,
        protoclust, Quartet, readxl, rmarkdown, Rcpp (>= 1.0.8), rgl,
        Rogue, spelling, TBRDist, testthat (>= 3.0), Ternary (>=
        1.1.2), TreeDistData (> 0.1.0), TreeSearch (>= 1.4.0), Umatrix,
        vdiffr (>= 1.0.0), withr,
LinkingTo: Rcpp, TreeTools (>= 2.1.0),
RdMacros: Rdpack
VignetteBuilder: knitr
Config/Needs/app/optional: uwot
Config/Needs/check: rcmdcheck
Config/Needs/coverage: covr
Config/Needs/memcheck: pkgdown, testthat
Config/Needs/metadata: codemetar
Config/Needs/revdeps: revdepcheck
Config/Needs/website: openssl, pkgdown, remotes, shinylive
Config/roxygen2/version: 8.0.0
Config/testthat/parallel: false
Config/testthat/edition: 3
SystemRequirements: C++17, pandoc-citeproc
ByteCompile: true
Encoding: UTF-8
Language: en-GB
X-schema.org-keywords: phylogenetics, tree-distance
Roxygen: list(markdown = TRUE)
Config/pak/sysreqs: cmake make libuv1-dev zlib1g-dev
Repository: https://phylotastic.r-universe.dev
Date/Publication: 2026-06-10 15:31:18 UTC
RemoteUrl: https://github.com/ms609/TreeDist
RemoteRef: HEAD
RemoteSha: 556796f652f0c496a5cdae11d3e901db47097dc5
NeedsCompilation: yes
Packaged: 2026-06-23 23:47:19 UTC; root
Author: Martin R. Smith [aut, cre, cph, prg] (ORCID:
    <https://orcid.org/0000-0001-5660-1727>),
  Roy Jonker [prg, cph] (LAP algorithm),
  Yong Yang [ctb, cph] (LAP algorithm),
  Yi Cao [ctb, cph] (LAP algorithm),
  Neil Kaye [cph] (Mercator image)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>