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 [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: Downloads: Reverse dependencies: Linking:Please use the canonical form https://CRAN.R-project.org/package=TreeDist to link to this page.
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