Package: TreeSearch
Title: Phylogenetic Tree Search Using Custom Optimality Criteria
Version: 0.3.0
Date: 2019-03-20
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 = "Emmanuel", family="Paradis", role = c("cph"),
                  comment = c(ORCID = "0000-0003-3092-2199")),
               person(given = "Klaus", family="Schliep", role = c("cph"),
                  comment = c(ORCID = "0000-0003-2941-0161")),
               person(given = "Martin", family="Brazeau", role = c("cph"), 
                  comment = c(ORCID = "0000-0002-0650-1282"))
            )
License: GPL (>= 3)
Copyright: Incorporates C/C++ code from: ape by Emmanuel Paradis;
        phangorn by Klaus Scheip <doi:10.1093/bioinformatics/btq706>;
        Morphy Phylogenetic Library by Martin Brazeau
        <https://github.com/mbrazeau/MorphyLib> (GPL3)
Description: Searches for phylogenetic trees that are optimal using a user-defined criterion. 
  Implements Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, and
  Successive Approximations (Farris, 1969) <doi:10.2307/2412182>.
  Handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith
  (2019) <doi:10.1093/sysbio/syy083>.
URL: https://github.com/ms609/TreeSearch
BugReports: https://github.com/ms609/TreeSearch/issues
Depends: R (>= 3.4.0)
Imports: ape (>= 5.0), clue, colorspace, memoise, phangorn (>= 2.2.1),
        R.cache, Rdpack, stats
Suggests: knitr, Rcpp, rmarkdown, shiny, testthat, xlsx
RdMacros: Rdpack
LazyData: true
ByteCompile: true
LinkingTo: Rcpp
Encoding: UTF-8
Language: en-GB
VignetteBuilder: knitr
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2019-03-21 07:47:44 UTC; ms609
Author: Martin R. Smith [aut, cre, cph]
    (<https://orcid.org/0000-0001-5660-1727>),
  Emmanuel Paradis [cph] (<https://orcid.org/0000-0003-3092-2199>),
  Klaus Schliep [cph] (<https://orcid.org/0000-0003-2941-0161>),
  Martin Brazeau [cph] (<https://orcid.org/0000-0002-0650-1282>)
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Repository: CRAN
Date/Publication: 2019-03-21 09:03:34 UTC
Built: R 3.4.4; x86_64-apple-darwin15.6.0; 2019-04-02 02:48:55 UTC; unix
Archs: TreeSearch.so.dSYM
