Package: TreeSearch
Title: Phylogenetic Analysis with Morphological Data
Version: 1.1.0
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: 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/,
        https://github.com/ms609/TreeSearch/
BugReports: https://github.com/ms609/TreeSearch/issues/
Depends: R (>= 3.5.0)
Imports: ape (>= 5.6), cli (>= 3.0), cluster, fastmatch (>= 1.1.3),
        future, phangorn (>= 2.2.1), promises, protoclust, Rcpp, Rdpack
        (>= 0.7), Rogue (> 2.0.0), shiny (>= 1.6.0), shinyjs, stats,
        TreeDist (>= 2.3.0), TreeTools (>= 1.6.0),
Suggests: knitr, Quartet, rmarkdown, spelling, testthat, vdiffr (>=
        1.0.0),
Config/Needs/coverage: covr
Config/Needs/github-actions: callr, pkgbuild, rcmdcheck
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++14
LazyData: true
ByteCompile: true
Encoding: UTF-8
Language: en-GB
VignetteBuilder: knitr
RoxygenNote: 7.1.2
NeedsCompilation: yes
Packaged: 2022-01-17 15:29:11 UTC; pjjg18
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: 2022-01-17 17:12:49 UTC
