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treenomial  

Comparison of Trees using a Tree Defining Polynomial
View on CRAN: Click here


Download and install treenomial package within the R console
Install from CRAN:
install.packages("treenomial")

Install from Github:
library("remotes")
install_github("cran/treenomial")

Install by package version:
library("remotes")
install_version("treenomial", "1.1.4")



Attach the package and use:
library("treenomial")
Maintained by
Matthew Gould
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-11-28
Latest Update: 2022-06-06
Description:
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.
How to cite:
Matthew Gould (2019). treenomial: Comparison of Trees using a Tree Defining Polynomial. R package version 1.1.4, https://cran.r-project.org/web/packages/treenomial. Accessed 21 Nov. 2024.
Previous versions and publish date:
1.0.0 (2019-11-28 16:10), 1.0.1 (2019-12-06 10:00), 1.1.1 (2019-12-07 00:40), 1.1.2 (2020-02-13 07:20), 1.1.3 (2020-10-05 17:00)
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Complete documentation for treenomial
Functions, R codes and Examples using the treenomial R package
Some associated functions: alignPoly . allTrees . plotExtremeTrees . polyDist . polyToDistMat . treeDist . treeJuliaSet . treeToDistMat . treeToPoly . wedge . 
Some associated R codes: RcppExports.R . allTrees.R . distFunctions.R . treeJuliaSet.R . treeToPoly.R . wedge.R .  Full treenomial package functions and examples
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