Package: TreeDist
Type: Package
Title: Calculate and Map Distances Between Phylogenetic Trees
Version: 2.11.1
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")
            )
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), colorspace, Rdpack (>= 0.7),
        shiny, shinyjs, TreeTools (>= 1.16),
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, testthat (>= 3.0), Ternary (>= 1.1.2),
        TreeDistData (> 0.1.0), TreeSearch (>= 1.4.0), Umatrix, uwot,
        vdiffr (>= 1.0.0),
LinkingTo: Rcpp, TreeTools (>= 1.16.1),
RdMacros: Rdpack
VignetteBuilder: knitr
Config/Needs/check: rcmdcheck
Config/Needs/coverage: covr
Config/Needs/memcheck: devtools
Config/Needs/metadata: codemetar
Config/Needs/revdeps: revdepcheck
Config/Needs/website: pkgdown
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
RoxygenNote: 7.3.3
NeedsCompilation: yes
Packaged: 2025-10-13 10:24:04 UTC; pjjg18
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)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Repository: CRAN
Date/Publication: 2025-10-13 13:40:06 UTC
Built: R 4.6.0; x86_64-w64-mingw32; 2025-12-02 05:00:27 UTC; windows
Archs: x64
