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: |
2.9.1 |
| Depends: |
R (≥ 3.4.0), stats |
| Imports: |
ape (≥ 5.0), cli (≥ 3.0), colorspace, memoise, Rdpack (≥
0.7), shiny, shinyjs, TreeTools (≥ 1.12.0) |
| 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: |
2024-09-07 |
| 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 |