taxodist
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. Path length, Wu-Palmer, and rank-based distances are also available, together with the taxonomic diversity and distinctness indices of Clarke and Warwick (1998) <doi:10.1046/j.1365-2664.1998.3540523.x> and their randomization test. Functions are provided for auditable name resolution, online or user-supplied lineage analysis, node ranks, 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.
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