Package: TreeSearch
Title: Phylogenetic Analysis with Discrete Character Data
Version: 1.8.0.9001
Authors@R: c(
    person(
      "Martin R.", 'Smith',
      email = "martin.smith@durham.ac.uk", 
      role = c("aut", "cre", "cph"), 
      comment = c(ORCID = "0000-0001-5660-1727")
    ),
    person(
      given = "Martin", family = "Brazeau",
      role = c("cph"),
      comment = c(ORCID = "0000-0002-0650-1282", "Morphy library")
    )
  )
License: GPL (>= 3)
Copyright: Incorporates C/C++ code from Morphy Phylogenetic Library by
        Martin Brazeau <https://github.com/mbrazeau/MorphyLib> (GPL3)
Description: Reconstruct phylogenetic trees from discrete data.
        Inapplicable character states are handled using the algorithm
        of Brazeau, Guillerme and Smith (2019)
        <doi:10.1093/sysbio/syy083> with the "Morphy" library, under
        equal or implied step weights. Contains a "shiny" user
        interface for interactive tree search and exploration of
        results, including character visualization, rogue taxon
        detection, tree space mapping, and cluster consensus trees
        (Smith 2022a, b) <doi:10.1093/sysbio/syab099>,
        <doi:10.1093/sysbio/syab100>. Profile Parsimony (Faith and
        Trueman, 2001) <doi:10.1080/10635150118627>, Successive
        Approximations (Farris, 1969) <doi:10.2307/2412182> and custom
        optimality criteria are implemented.
URL: https://ms609.github.io/TreeSearch/ (doc),
        https://github.com/ms609/TreeSearch/ (devel)
BugReports: https://github.com/ms609/TreeSearch/issues/
Depends: R (>= 4.0)
Imports: abind, ape (>= 5.6), base64enc, cli (>= 3.0), cluster,
        colorspace, fastmap, fastmatch (>= 1.1.3), fs, future,
        PlotTools, promises, protoclust, Rcpp, Rdpack (>= 0.7), Rogue
        (> 2.0.0), shiny (>= 1.6.0), shinyjs, stats, stringi, TreeDist
        (>= 2.6.3), TreeTools (>= 1.16),
Suggests: knitr, phangorn (>= 2.2.1), Quartet, readxl, rmarkdown,
        shinytest, spelling, testthat, vdiffr (>= 1.0.0),
Config/Needs/check: callr, pkgbuild, rcmdcheck,
Config/Needs/coverage: covr, spelling
Config/Needs/memcheck: devtools, remotes
Config/Needs/metadata: codemeta
Config/Needs/revdeps: revdepcheck
Config/Needs/website: curl, igraph, pkgdown,
Config/roxygen2/version: 8.0.0
RdMacros: Rdpack
LinkingTo: Rcpp, TreeTools,
SystemRequirements: C++17
LazyData: true
ByteCompile: true
Encoding: UTF-8
Language: en-GB
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev zlib1g-dev
Repository: https://ms609.r-universe.dev
Date/Publication: 2026-07-03 12:07:36 UTC
RemoteUrl: https://github.com/ms609/treesearch
RemoteRef: HEAD
RemoteSha: 4c88ce1ac9887a4aa2f11de4826f0b5275ce04c1
NeedsCompilation: yes
Packaged: 2026-07-03 12:13:42 UTC; root
Author: Martin R. Smith [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0001-5660-1727>),
  Martin Brazeau [cph] (ORCID: <https://orcid.org/0000-0002-0650-1282>,
    Morphy library)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>