Package: treenomial 1.1.4

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

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treenomial.pdf |treenomial.html
treenomial/json (API)
NEWS

# Install 'treenomial' in R:
install.packages('treenomial', repos = c('https://gouldmatt.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/gouldmatt/treenomial/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

3.43 score 2 stars 27 scripts 212 downloads 10 exports 7 dependencies

Last updated 2 years agofrom:a2d20b737e. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 13 2024
R-4.5-win-x86_64NOTENov 13 2024
R-4.5-linux-x86_64NOTENov 13 2024
R-4.4-win-x86_64NOTENov 13 2024
R-4.4-mac-x86_64NOTENov 13 2024
R-4.4-mac-aarch64NOTENov 13 2024
R-4.3-win-x86_64NOTENov 13 2024
R-4.3-mac-x86_64NOTENov 13 2024
R-4.3-mac-aarch64NOTENov 13 2024

Exports:alignPolyallTreesplotExtremeTreespolyDistpolyToDistMattreeDisttreeJuliaSettreeToDistMattreeToPolywedge

Dependencies:apedigestlatticenlmeRcppRcppArmadilloRcppThread