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Provides functionality for creation and comparison of polynomials that uniquely describe trees as introduced in Liu (2019, <doi:10.48550/arXiv.1904.03332>). The core method converts rooted unlabeled phylo objects from 'ape' to the tree defining polynomials described with coefficient matrices. Additionally, a conversion for rooted binary trees with binary trait labels is also provided. Once the polynomials of trees are calculated there are functions to calculate distances, distance matrices and plot different distance trees from a target tree. Manipulation and conversion to the tree defining polynomials is implemented in C++ with 'Rcpp' and 'RcppArmadillo'. Furthermore, parallel programming with 'RcppThread' is used to improve performance converting to polynomials and calculating distances.
| Version: | 1.1.4 |
| Depends: | R (≥ 3.5.0) |
| Imports: | Rcpp (≥ 1.0.1), ape, methods |
| LinkingTo: | Rcpp, RcppArmadillo, RcppThread (≥ 2.1.3) |
| Suggests: | knitr, rmarkdown, testthat |
| Published: | 2022-06-06 |
| DOI: | 10.32614/CRAN.package.treenomial |
| Author: | Matthew Gould [aut, cre], Pengyu Liu [ctb], Caroline Colijn [ctb] |
| Maintainer: | Matthew Gould <mgould at sfu.ca> |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: | https://github.com/gouldmatt/treenomial |
| NeedsCompilation: | yes |
| Materials: | README NEWS |
| CRAN checks: | treenomial results |
| Reference manual: | treenomial.pdf |
| Package source: | treenomial_1.1.4.tar.gz |
| Windows binaries: | r-devel: treenomial_1.1.4.zip, r-release: treenomial_1.1.4.zip, r-oldrel: treenomial_1.1.4.zip |
| macOS binaries: | r-release (arm64): treenomial_1.1.4.tgz, r-oldrel (arm64): treenomial_1.1.4.tgz, r-release (x86_64): treenomial_1.1.4.tgz, r-oldrel (x86_64): treenomial_1.1.4.tgz |
| Old sources: | treenomial archive |
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