Package: TreeDist
Type: Package
Title: Calculate and Map Distances Between Phylogenetic Trees
Version: 2.1.0
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")),
             person("Yong", "Yang", email="yongyanglink@gmail.com",
                    role=c("ctb", "cph")),
             person("Yi", "Cao", role=c("ctb", "cph"))
            )
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>;
  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, for
  calculating the median of sets of trees, and for computing the information
  content of trees and splits.
Copyright: Incorporates Jonker-Volgenant Linear Assignment Problem
        implementation by Roy Jonker, modified by Yong Yang after 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 (>= 3.4.0), stats
Imports: ape (>= 5.0), colorspace, memoise, phangorn (>= 2.2.1), Rdpack
        (>= 0.7), shiny, shinyjs, TreeTools (> 1.3.1)
Suggests: bookdown, cluster, ggplot2, kdensity, knitr, MASS,
        protoclust, Quartet, readxl, rmarkdown, Rcpp, rgl, testthat,
        Ternary (>= 1.1.2), TreeDistData (> 0.1.0), TreeSearch,
        Umatrix, vdiffr (>= 1.0.0)
LinkingTo: Rcpp, TreeTools
RdMacros: Rdpack
VignetteBuilder: knitr
Config/Needs/coverage: covr
Config/Needs/metadata: codemetar
Config/Needs/website: pkgdown
SystemRequirements: C++14
ByteCompile: true
Encoding: UTF-8
Language: en-GB
X-schema.org-keywords: phylogenetics, tree-distance
RoxygenNote: 7.1.1
NeedsCompilation: yes
Packaged: 2021-07-09 18:54:51 UTC; ms609
Author: Martin R. Smith [aut, cre, cph, prg]
    (<https://orcid.org/0000-0001-5660-1727>),
  Roy Jonker [prg, cph],
  Yong Yang [ctb, cph],
  Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Repository: CRAN
Date/Publication: 2021-07-12 07:50:05 UTC
