taxodist 0.1.0

• Initial release
• Compute taxonomic distances between any two taxa using The Taxonomicon
• Session-level caching for lineage data to minimize network requests
• Functions: taxo_distance(), mrca(), distance_matrix(), closest_relative(), compare_lineages(), shared_clades(), is_member(), filter_clade(), lineage_depth(), check_coverage(), clear_cache()

taxodist 0.2.0

New functions

• taxo_cluster(): hierarchical clustering of taxa by taxonomic distance.
• taxo_ordinate(): ordination (PCoA) of taxa in taxonomic distance space.
• save_cache(): serialises the session lineage cache to an .rds file.
• load_cache(): restores a previously saved cache, avoiding redundant network requests.
• taxo_path(): returns the full node-by-node path between two taxa as a tidy data frame, ascending from taxon A to their MRCA and descending to taxon B.

Documentation

• Added a new vignette (Statistical Applications of taxodist) demonstrating the integration of taxodist with ape (tree plotting) and vegan (taxonomic distinctness, Mantel tests, and PERMANOVA).

Minor improvements

• Added vegan to Suggests in DESCRIPTION.
• Documented the compatibility of distance_matrix() output with vegan functions (taxondive(), mantel(), adonis2()).
• Documented the conversion of taxo_cluster() results into phylo objects using ape::as.phylo().

Bug fixes

• Fixed incorrect MRCA computation caused by unnamed crown nodes ([crown]) being matched across different lineages as if they were the same ancestor.
• Fixed parsing of Taxonomicon rank prefixes (Cohort, Subcohort, Magnorder, Grandorder, Parvorder, Legion) that were being retained as bare rank names instead of the actual clade names (e.g., Placentalia, Boreoeutheria, Galloanserae).