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>; the Hierarchical Mutual Information (Perotti et al. 2015) <doi:10.1103/PhysRevE.92.062825>; 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: | 2.11.1 |
| Depends: | R (≥ 4.0), stats |
| Imports: | ape (≥ 5.0),cli (≥ 3.0),colorspace,Rdpack (≥ 0.7),shiny,shinyjs,TreeTools (≥ 1.16) |
| LinkingTo: | Rcpp,TreeTools (≥ 1.16.1) |
| 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: | 2025-10-13 |
| DOI: | 10.32614/CRAN.package.TreeDist |
| Author: | Martin R. Smith [aut, cre, cph, prg], Roy Jonker [prg, cph] (LAP algorithm), Yong Yang [ctb, cph] (LAP algorithm), Yi Cao [ctb, cph] (LAP algorithm) |
| 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 byRoy 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 |