[aut, cre, cph, prg],
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]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 the landscape of a tree space, and for calculating the median of a set of trees under any distance metric.
| Version: | 2.0.3 |
| Depends: | R (≥ 3.4.0), stats |
| Imports: | ape (≥ 5.0), colorspace, memoise, phangorn (≥ 2.2.1), Rdpack, shiny, shinyjs, TreeTools (> 1.3.1) |
| LinkingTo: | Rcpp, TreeTools |
| Suggests: | bookdown, cluster, kdensity, knitr, MASS, protoclust, Quartet, readxl, rmarkdown, Rcpp, rgl, testthat, Ternary (≥ 1.1.2), TreeDistData (> 0.1.0), TreeSearch, vdiffr, viridisLite |
| Published: | 2021-01-31 |
| 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: | Incorporates Jonker-Volgenant Linear Assignment Problem implementation by Roy Jonker, modified by Yong Yang after Yi Cao. |
| URL: | https://ms609.github.io/TreeDist/, https://github.com/ms609/TreeDist/ |
| NeedsCompilation: | yes |
| SystemRequirements: | C++14 |
| Additional_repositories: | https://ms609.github.io/packages/ |
| Language: | en-GB |
| Citation: | TreeDist citation info |
| Materials: | NEWS |
| CRAN checks: | TreeDist results |
| Reference manual: | TreeDist.pdf |
| Vignettes: |
Generalized Robinson-Foulds distances Extending the Robinson-Foulds metric Calculate tree similarity with 'TreeDist' Comparing splits using information theory Tree space & landscape analysis Contextualizing tree distances |
| Package source: | TreeDist_2.0.3.tar.gz |
| Windows binaries: | r-devel: TreeDist_2.0.3.zip, r-release: TreeDist_2.0.3.zip, r-oldrel: TreeDist_2.0.3.zip |
| macOS binaries: | r-release: TreeDist_2.0.3.tgz, r-oldrel: TreeDist_2.0.3.tgz |
| Old sources: | TreeDist archive |
| Reverse imports: | TBRDist |
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