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 auditable name resolution, online or user-supplied lineage analysis, clade membership, pairwise and matrix distance calculation, hierarchical clustering, principal coordinates analysis, portable JSON analysis bundles, 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: | 0.8.0 |
| 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), jsonlite (≥ 1.8.0), utils, stats, graphics |
| Suggests: | testthat (≥ 3.0.0), mockery, knitr, rmarkdown, xml2, ape, vegan, webmockr |
| Published: | 2026-09-24 |
| 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 for online taxonomy retrieval |
| 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_0.8.0.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_0.8.0.tgz, r-release (x86_64): taxodist_0.8.0.tgz, r-oldrel (x86_64): taxodist_0.8.0.tgz |
| Old sources: | taxodist archive |
Linking:
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