DESCRIPTION

Package: TreeSearch
Title: Phylogenetic Analysis with Discrete Character Data
Version: 1.5.1.9000
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")
    )
  )
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 (>= 3.5.0)
Imports: 
  ape (>= 5.6),
  cli (>= 3.0),
  cluster,
  fastmatch (>= 1.1.3),
  fs,
  future,
  PlotTools,
  promises,
  protoclust,
  Rcpp,
  Rdpack (>= 0.7),
  Rogue (> 2.0.0),
  shiny (>= 1.6.0),
  shinyjs,
  stats,
  TreeDist (>= 2.6.3),
  TreeTools (>= 1.10.0),
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
Config/Needs/metadata: codemeta
Config/Needs/revdeps: revdepcheck
Config/Needs/website: 
  curl,
  igraph,
  pkgdown,
RdMacros: Rdpack
LinkingTo:
  Rcpp,
  TreeTools,
SystemRequirements: C++17
LazyData: true
ByteCompile: true
Encoding: UTF-8
Language: en-GB
VignetteBuilder: knitr
RoxygenNote: 7.3.1
Roxygen: list(markdown = TRUE)