Package: treenomial 1.1.4
Matthew Gould
treenomial: 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, <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.
Authors:
treenomial_1.1.4.tar.gz
treenomial_1.1.4.tar.gz(r-4.5-noble)treenomial_1.1.4.tar.gz(r-4.4-noble)
treenomial_1.1.4.tgz(r-4.4-emscripten)treenomial_1.1.4.tgz(r-4.3-emscripten)
treenomial.pdf |treenomial.html✨
treenomial/json (API)
NEWS
| # Install 'treenomial' in R: |
| install.packages('treenomial', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/gouldmatt/treenomial/issues
Last updated 3 years agofrom:48233d6c67. Checks:OK: 1 NOTE: 1. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 30 2024 |
| R-4.5-linux-x86_64 | NOTE | Dec 30 2024 |
Exports:alignPolyallTreesplotExtremeTreespolyDistpolyToDistMattreeDisttreeJuliaSettreeToDistMattreeToPolywedge
Dependencies:apedigestlatticenlmeRcppRcppArmadilloRcppThread
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Align various types of coefficient matrices | alignPoly |
| Calculate all full unordered m-ary trees up to n tips | allTrees |
| Plot the min/max distance trees from a target tree | plotExtremeTrees |
| Calculates the distance between coefficient matrices | polyDist |
| Calculates the distance matrix from a list coefficient matrices | polyToDistMat |
| Calculates the distance between trees | treeDist |
| Plots a Julia Set for a tree | treeJuliaSet |
| Calculates the distance matrix from a list of phylo objects | treeToDistMat |
| Convert trees to coefficient matrices | treeToPoly |
| Performs the wedge operation | wedge |
