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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 ORCID iD [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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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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