Description: Implementation of the TreeRank methodology for building
tree-based ranking rules for bipartite ranking through ROC
Depends: rpart, tcltk, igraph, colorspace, tkrplot, kernlab, coin

Depends: rpart, tcltk, igraph, colorspace, tkrplot, kernlab, coin,

Title: Phylogenetic Tree Search Using Custom Optimality Criteria
Copyright: Incorporates C code from the ape and phangorn packages by
Emmanuel Paradis and Klaus Schliep. Code is copied rather than
linked in the absence of a suitable R interface.
Description: Searches for phylogenetic trees that are optimal using a user-defined criterion. Employed in Brazeau Guillerme and Smith (2017) <doi:10.1101/209775>.
Imports: ape (>= 4.1), phangorn (>= 2.2.1)

Copyright: Incorporates C code from: ape by Emmanuel Paradis; Morphy
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>.
Imports: ape (>= 5.0), memoise, phangorn (>= 2.2.1), R.cache, Rdpack,
Suggests: knitr, rmarkdown, testthat, xlsx

Suggests: knitr, rmarkdown, shiny, testthat, xlsx

Imports: ape (>= 5.0), colorspace, gmp, memoise, phangorn (>= 2.2.1),

person(given = "Emmanuel", family="Paradis", role = c("cph"),
person(given = "Klaus", family="Schliep", role = c("cph"),
person(given = "Martin", family="Brazeau", role = c("cph"),
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
Handles inapplicable data using the algorithm of Brazeau, Guillerme and Smith

Suggests: knitr, Rcpp, rmarkdown, shiny, testthat, xlsx

Imports: ape (>= 5.0), clue, colorspace, memoise, phangorn (>= 2.2.1),

Copyright: Incorporates C/C++ code from Morphy Phylogenetic Library by
Description: Searches for phylogenetic trees that are optimal using a
Handles inapplicable data using the algorithm of
Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083>.
Implements Profile Parsimony (Faith and Trueman, 2001)
<doi:10.1080/10635150118627>, and Successive Approximations (Farris, 1969)
Imports: ape (>= 5.0), phangorn (>= 2.2.1), R.cache, Rdpack, stats,