NEWS.md

In taxodist: Taxonomic Distance and Phylogenetic Lineage Computation

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).

taxodist 0.3.0

New features

• taxo_search(): Added a new interactive search function that queries The Taxonomicon and returns a tidy data frame of all available IDs, ranks, and authors for a given taxon name.
• Direct ID Support: get_lineage() and all distance functions (e.g., taxo_distance(), distance_matrix()) now accept Taxonomicon numeric IDs. This provides a fallback for computing distances when homonyms or historical ranks cannot be disambiguated by name alone.

Network Handling

• Added a 30-second timeout to all HTTP requests to prevent the R session from hanging indefinitely when The Taxonomicon servers are overloaded.
• Network failures, offline servers, or bad HTTP statuses now immediately emit a clear, informative warning to the user rather than failing silently.

Bug fixes

• Extended rank-prefix filter to remove additional bare rank tokens that were being retained as spurious lineage nodes: Subgenus, Section, Division, Subdivision, Supercohort, Infracohort, Subsection, Candidatus, Parvphylum, Branch, and Go to (a navigation artefact from The Taxonomicon page layout).
• Duplicate lineage nodes originating from data-quality issues in The Taxonomicon (e.g. Uropygi appearing twice in Thelyphonida, Myxomycetes appearing twice in Physarum) are now collapsed to a single occurrence. A warning is emitted when deduplication occurs so the user is aware of the upstream data issue.
• get_taxonomicon_id() now collects all biological matches for a taxon name before returning, and emits a warning when multiple valid biological entries are found in The Taxonomicon. This surfaces homonym ambiguity (e.g. Nereis matching both a polychaete worm and a butterfly genus) that was previously silent.
• get_taxonomicon_id() now properly follows taxonomic redirects and removes interface noise (N|T|P...) from warnings.
• When multiple biological entries are found (e.g. Bacteria), the warning now lists all available numeric IDs without duplicates, allowing users to make an informed choice.
• Made lineage parsing more robust by strictly truncating any philosophical or pre-basal nodes (e.g. organisms) appearing before Biota.
• Added validation to get_lineage_by_id() to silently return NULL for non-numeric strings, preventing upstream server fallback errors.
• Fixed a lineage parsing issue where the parent Genus was erroneously truncated from species-level queries. Distances and Most Recent Common Ancestors (MRCAs) between congeneric species are now computed accurately.
• Fixed an issue where taxonomic author names enclosed in double quotes (e.g., "Redtenbacher, 1906") were evading the lineage cleaning pipeline and being erroneously retained as part of the clade name.

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