TreeDist: Calculate and Map Distances Between Phylogenetic Trees

Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Includes tools for visualizing mappings of tree space (Smith 2022) <doi:10.1093/sysbio/syab100>, for identifying islands of trees (Silva and Wilkinson 2021) <doi:10.1093/sysbio/syab015>, for calculating the median of sets of trees, and for computing the information content of trees and splits.

Version: 2.9.2
Depends: R (≥ 3.4.0), stats
Imports: ape (≥ 5.0), cli (≥ 3.0), colorspace, memoise, Rdpack (≥ 0.7), shiny, shinyjs, TreeTools (≥ 1.13.0)
LinkingTo: Rcpp, TreeTools
Suggests: bookdown, cluster, ggplot2, hypervolume, kdensity, knitr, MASS, parallel, phangorn (≥ 2.2.1), plotly, PlotTools, protoclust, Quartet, readxl, rmarkdown, Rcpp (≥ 1.0.8), rgl, Rogue, spelling, testthat (≥ 3.0), Ternary (≥ 1.1.2), TreeDistData (> 0.1.0), TreeSearch (≥ 1.4.0), Umatrix, uwot, vdiffr (≥ 1.0.0)
Published: 2025-01-11
DOI: 10.32614/CRAN.package.TreeDist
Author: Martin R. Smith ORCID iD [aut, cre, cph, prg], Roy Jonker [prg, cph], Yong Yang [ctb, cph], Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith at durham.ac.uk>
BugReports: https://github.com/ms609/TreeDist/issues/
License: GPL (≥ 3)
Copyright: Jonker-Volgenant Linear Assignment Problem implementation by Roy Jonker modified by Yong Yang and Yi Cao.
URL: https://ms609.github.io/TreeDist/, https://github.com/ms609/TreeDist/
NeedsCompilation: yes
SystemRequirements: C++17, pandoc-citeproc
Additional_repositories: https://ms609.github.io/packages/
Language: en-GB
Citation: TreeDist citation info
Materials: NEWS
In views: Optimization, Phylogenetics
CRAN checks: TreeDist results

Documentation:

Reference manual: TreeDist.pdf
Vignettes: Generalized Robinson-Foulds distances (source, R code)
Extending the Robinson-Foulds metric (source, R code)
Calculate tree similarity with 'TreeDist' (source, R code)
Comparing sets of trees from different analyses (source, R code)
Trees with different leaves (source, R code)
Comparing splits using information theory (source, R code)
Analysing landscapes of phylogenetic trees (source, R code)
Tree space analysis (source, R code)
Contextualizing tree distances (source, R code)

Downloads:

Package source: TreeDist_2.9.2.tar.gz
Windows binaries: r-devel: TreeDist_2.9.2.zip, r-release: TreeDist_2.9.2.zip, r-oldrel: TreeDist_2.9.2.zip
macOS binaries: r-devel (arm64): TreeDist_2.9.2.tgz, r-release (arm64): TreeDist_2.9.2.tgz, r-oldrel (arm64): TreeDist_2.9.2.tgz, r-devel (x86_64): TreeDist_2.9.2.tgz, r-release (x86_64): TreeDist_2.9.2.tgz, r-oldrel (x86_64): TreeDist_2.9.2.tgz
Old sources: TreeDist archive

Reverse dependencies:

Reverse imports: Rogue, TBRDist, TreeSearch

Linking:

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