Package: TreeSearch
Title: Phylogenetic Tree Search Using Custom Optimality Criteria
Version: 0.1.2
Date: 2018-03-19
Authors@R: c(person("Martin R.", 'Smith',
                  email="martins@gmail.com", 
                  role=c("aut", "cre", "cph"), 
                  comment=c(ORCID = "0000-0001-5660-1727")),
               person(given = "Emmanuel", family="Paradis",
               role = c("cph")),
               person(given = "Martin", family="Brazeau",
               role = c("cph"))
            )
License: GPL (>= 3)
Copyright: Incorporates C code from:
   ape by Emmanuel Paradis;
   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 (2017) <doi:10.1101/209775>.
URL: https://github.com/ms609/TreeSearch
BugReports: https://github.com/ms609/TreeSearch/issues
Depends: R (>= 3.4.0)
Imports: 
    ape (>= 5.0),
    memoise,
    phangorn (>= 2.2.1),
    R.cache,
    Rdpack,
    stats
Suggests:
    knitr,
    rmarkdown,
    shiny,
    testthat,
    xlsx
RdMacros: Rdpack
LazyData: true
ByteCompile: true
VignetteBuilder: knitr
RoxygenNote: 6.0.1
