DESCRIPTION

Package: TreeDist
Type: Package
Title: Calculate and Map Distances Between Phylogenetic Trees
Version: 2.9.1
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>.
  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 (>= 3.4.0),
  stats,
Imports: 
  ape (>= 5.0),
  cli (>= 3.0),
  colorspace,
  memoise,
  Rdpack (>= 0.7),
  shiny,
  shinyjs,
  TreeTools (>= 1.12.0),
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,
  testthat (>= 3.0),
  Ternary (>= 1.1.2),
  TreeDistData (> 0.1.0),
  TreeSearch (>= 1.4.0),
  Umatrix,
  uwot,
  vdiffr (>= 1.0.0),
LinkingTo: 
  Rcpp,
  TreeTools,
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: 7.3.1
Roxygen: list(markdown = TRUE)