taxodist: Taxonomic Hierarchy Distances and Lineage Analysis
Computes distances between taxonomic hierarchy nodes using lineage data retrieved from The Taxonomicon <http://taxonomicon.taxonomy.nl>. For distinct nodes, distance is defined as the reciprocal of the depth of their most recent common ancestor; identical nodes have distance zero. This definition yields an ultrametric within each connected hierarchy. Functions are provided for lineage retrieval and comparison, clade membership, pairwise and matrix distance calculation, hierarchical clustering, principal coordinates analysis, and cache management. Distance matrices are returned as base R 'dist' objects. The distances represent classification depth rather than evolutionary time or phylogenetic branch length.
| Version: | 0.7.0 |
| Depends: | R (≥ 4.1.0) |
| Imports: | httr (≥ 1.4.0), rvest (≥ 1.0.0), stringr (≥ 1.4.0), purrr (≥ 0.3.0), cli (≥ 3.0.0), utils, stats, graphics |
| Suggests: | testthat (≥ 3.0.0), mockery, knitr, rmarkdown, xml2, ape, vegan, webmockr |
| Published: | 2026-08-28 |
| DOI: | 10.32614/CRAN.package.taxodist |
| Author: | Rodrigo Fonseca Villa
 [aut, cre] |
| Maintainer: | Rodrigo Fonseca Villa <rodrigo03.villa at gmail.com> |
| BugReports: | https://github.com/rodrigosqrt3/taxodist/issues |
| License: | GPL (≥ 3) |
| URL: | https://github.com/rodrigosqrt3/taxodist |
| NeedsCompilation: | no |
| SystemRequirements: | internet access |
| Language: | en-US |
| Citation: | taxodist citation info |
| Materials: | NEWS |
| In views: | Phylogenetics |
| CRAN checks: | taxodist results |
Documentation:
| Reference manual: | taxodist.html , taxodist.pdf |
| Vignettes: |
Introduction to taxodist (source, R code) Methodological Notes and Limitations (source, R code) Statistical Applications of taxodist (source, R code) |
Downloads:
| Package source: | taxodist_0.7.0.tar.gz |
| Windows binaries: | r-devel: taxodist_0.7.0.zip, r-release: taxodist_0.7.0.zip, r-oldrel: taxodist_0.7.0.zip |
| macOS binaries: | r-release (arm64): taxodist_0.7.0.tgz, r-oldrel (arm64): taxodist_0.7.0.tgz, r-release (x86_64): taxodist_0.7.0.tgz, r-oldrel (x86_64): taxodist_0.7.0.tgz |
| Old sources: | taxodist archive |
Linking:
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