taxodist-package: taxodist: Taxonomic Distance and Phylogenetic Lineage...

In taxodist: Taxonomic Distance and Phylogenetic Lineage Computation

taxodist: Taxonomic Distance and Phylogenetic Lineage Computation

Description

taxodist computes phylogenetic distances between any two taxa using hierarchical lineage data retrieved from The Taxonomicon (taxonomy.nl), a comprehensive curated classification of all life based on Systema Naturae 2000.

Core functions

• get_lineage() — retrieve the full lineage of any taxon

• taxo_distance() — compute the tree metric distance between two taxa

• mrca() — find the most recent common ancestor

• distance_matrix() — compute all pairwise distances for a set of taxa

• closest_relative() — find the closest relative among candidates

• compare_lineages() — print a side-by-side lineage comparison

• shared_clades() — list clades shared between two taxa

• is_member() — test clade membership

• filter_clade() — filter taxa by clade membership

• check_coverage() — check Taxonomicon coverage for a list of taxa

• lineage_depth() — get the lineage depth of a taxon

• clear_cache() — clear the session lineage cache

Mathematical background

The distance metric is based on the depth of the most recent common ancestor (MRCA):

d(A, B) = \frac{1}{\text{depth}(\text{MRCA}(A,B))}

The deeper the shared ancestor, the smaller the distance. This metric ensures that taxa sharing the same MRCA are always equidistant from any third taxon, regardless of lineage depth below the split — a key biological correctness property absent from Jaccard-based approaches.

Data source

All lineage data is sourced from The Taxonomicon (taxonomy.nl), based on Systema Naturae 2000 by S.J. Brands (1989 onwards). Please cite this resource when using taxodist in published work.

Author(s)

Maintainer: Rodrigo Fonseca Villa [e-mail] (ORCID)

References

Brands, S.J. (1989 onwards). Systema Naturae 2000. Amsterdam, The Netherlands. Retrieved from The Taxonomicon, http://taxonomicon.taxonomy.nl.

See Also

Useful links:

• https://github.com/rodrigosqrt3/taxodist

• Report bugs at https://github.com/rodrigosqrt3/taxodist/issues

taxodist documentation built on May 6, 2026, 1:06 a.m.