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. Path length, Wu-Palmer, and rank-based distances are also available, together with the taxonomic diversity and distinctness indices of Clarke and Warwick (1998) 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.