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, matrix, and cross-set distance calculation, classification trees with named clades, hierarchical clustering, principal coordinates analysis, portable and comparable 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.


Reference manual

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install.packages("taxodist")

0.9.0 by Rodrigo Fonseca Villa, 3 days ago


https://github.com/rodrigosqrt3/taxodist


Report a bug at https://github.com/rodrigosqrt3/taxodist/issues


Browse source code at https://github.com/cran/taxodist


Authors: Rodrigo Fonseca Villa [aut, cre] (ORCID:


Documentation:   PDF Manual  


GPL (>= 3) license


Imports httr, rvest, stringr, cli, jsonlite, utils, stats, graphics, tools

Suggests testthat, mockery, knitr, rmarkdown, xml2, ape, vegan

System requirements: internet access for online taxonomy retrieval


See at CRAN