Package: TreeSearch
Title: Phylogenetic Tree Search Using Custom Optimality Criteria
Version: 1.0.0
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: Search for phylogenetic trees that are optimal using a
  user-defined criterion.
  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.
  Handles inapplicable data using the algorithm of Brazeau, Guillerme and
  Smith (2019) <doi:10.1093/sysbio/syy083> using the "Morphy" library.
  Implements Profile Parsimony (Faith and Trueman, 2001) 
  <doi:10.1080/10635150118627>, and Successive Approximations (Farris, 1969) 
  <doi:10.2307/2412182>.
URL: https://ms609.github.io/TreeSearch/,
        https://github.com/ms609/TreeSearch/
BugReports: https://github.com/ms609/TreeSearch/issues/
Depends: R (>= 3.5.0)
Imports: ape (>= 5.1.2), cli (>= 3.0), cluster, fastmatch (>= 1.1.3),
        future, phangorn (>= 2.2.1), promises, protoclust, Rcpp, Rdpack
        (>= 0.7), Rogue (> 1.0.0), shiny, shinyjs, stats, TreeDist (>
        2.0.3), TreeTools (>= 1.5.0),
Suggests: knitr, rmarkdown, Quartet, testthat, vdiffr (>= 1.0.0),
Config/Needs/coverage: covr
Config/Needs/github-actions: callr, pkgbuild, rcmdcheck
Config/Needs/memcheck: devtools
Config/Needs/metadata: codemetar
Config/Needs/revdeps: revdepcheck
Config/Needs/website: curl, igraph, pkgdown
RdMacros: Rdpack
LinkingTo: Rcpp, TreeTools
SystemRequirements: C++14
LazyData: true
ByteCompile: true
Encoding: UTF-8
Language: en-GB
VignetteBuilder: knitr
RoxygenNote: 7.1.2
NeedsCompilation: yes
Packaged: 2021-09-20 10:33:44 UTC; ms609
Author: Martin R. Smith [aut, cre, cph]
    (<https://orcid.org/0000-0001-5660-1727>),
  Martin Brazeau [cph] (<https://orcid.org/0000-0002-0650-1282>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Repository: CRAN
Date/Publication: 2021-09-22 10:10:19 UTC
