Comparison of Trees using a Tree Defining Polynomial

Provides functionality for creation and comparison of polynomials that uniquely describe trees as introduced in Liu (2019, ). 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.


Reference manual

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1.0.0 by Matthew Gould, 7 days ago

Browse source code at

Authors: Matthew Gould [aut, cre] , Pengyu Liu [ctb] , Caroline Colijn [ctb]

Documentation:   PDF Manual  

GPL (>= 2) license

Imports Rcpp, ape

Suggests knitr, rmarkdown, testthat

Linking to Rcpp, RcppArmadillo, RcppThread

See at CRAN