Package: TreeDist
Type: Package
Title: Distances Between Phylogenetic Trees
Version: 1.1.1
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")),
             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>.
  Calculates the median of a set of trees under any distance metric.
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
Depends: R (>= 3.4.0), stats
Imports: ape (>= 5.0), colorspace, memoise, phangorn (>= 2.2.1),
        TreeTools (>= 1.1.0)
Suggests: bookdown, cluster, kdensity, knitr, MASS, Quartet, rmarkdown,
        Rcpp, Rdpack, testthat, Ternary (>= 1.1.2), TreeDistData (>
        0.1.0), TreeSearch, vdiffr
Additional_repositories: https://ms609.github.io/packages
RdMacros: Rdpack
VignetteBuilder: knitr
LinkingTo: Rcpp
SystemRequirements: C++11
LazyData: true
ByteCompile: true
Encoding: UTF-8
Language: en-GB
X-schema.org-keywords: phylogenetics, tree-distance
RoxygenNote: 7.1.1
NeedsCompilation: yes
Packaged: 2020-07-09 13:16:53 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: 2020-07-10 15:40:02 UTC
Built: R 4.0.2; x86_64-w64-mingw32; 2020-08-02 12:42:47 UTC; windows
Archs: i386, x64
