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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: | 2.8.0 |
Depends: | R (≥ 3.4.0), stats |
Imports: | ape (≥ 5.0), cli (≥ 3.0), colorspace, memoise, Rdpack (≥ 0.7), shiny, shinyjs, TreeTools (≥ 1.11.1.9004) |
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: | 2024-07-26 |
DOI: | 10.32614/CRAN.package.TreeDist |
Author: | Martin R. Smith |
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 |
Package source: | TreeDist_2.8.0.tar.gz |
Windows binaries: | r-devel: TreeDist_2.8.0.zip, r-release: TreeDist_2.8.0.zip, r-oldrel: TreeDist_2.8.0.zip |
macOS binaries: | r-release (arm64): TreeDist_2.8.0.tgz, r-oldrel (arm64): TreeDist_2.8.0.tgz, r-release (x86_64): TreeDist_2.8.0.tgz, r-oldrel (x86_64): TreeDist_2.8.0.tgz |
Old sources: | TreeDist archive |
Reverse imports: | Rogue, TBRDist, TreeSearch |
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These binaries (installable software) and packages are in development.
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