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 0.4.0

New features

• cache_info(): inspects the current session cache, reporting the number of cached lineages and IDs, total memory used, and the names of all taxa whose lineages are stored. Returns a named list invisibly for programmatic use.
• focal_distances(): computes taxonomic distances from a single focal taxon to all members of a community vector. Returns a sorted data frame with columns taxon, distance, mrca, and mrca_depth, making it easy to identify the closest and most distant relatives of a focal species in a community context.

Bug fixes

• Fixed a lineage parsing bug where taxa with Subphylum and Infraphylum rank prefixes (e.g., Craniata, Vertebrata) were being incorrectly discarded. The dagger symbol (†) is now stripped before rank prefixes are removed, ensuring that prefixed names like Subphylum † Craniata are correctly parsed to Craniata rather than falling through as bare rank tokens. Subphylum and Infraphylum have been removed from bare_ranks accordingly.
• Fixed parsing of auct. author annotations (e.g., Subphylum Craniata auct.) that were preventing rank-prefixed names from being correctly cleaned.
• Fixed intermediate clades being silently dropped from lineages when their author strings contained ampersands, hyphens (e.g., Cavalier-Smith), or trailing commas without a year (e.g., Romeriida Gauthier,). The author removal pipeline now handles these patterns correctly.
• Fixed a bug where the dagger extinction marker (†) appearing between a rank prefix and a taxon name (e.g., Family † Dromaeosauridae) caused the taxon to be lost entirely. Dagger removal now precedes all other cleaning steps.

taxodist 0.5.0

New features

• taxobase: Added a built-in reference dataset containing 50 taxonomic clades. The dataset includes pre-computed distance matrices, lineage paths, search outputs, and coverage vectors. It acts as a complete offline fallback, allowing package examples, vignettes, and unit tests to run instantly without requiring a network connection to The Taxonomicon.

Bug fixes

• Fixed a bug where any taxon whose name contains the substring “planet” (e.g. Periplaneta) was incorrectly discarded by the astronomical homonym filter in get_taxonomicon_id() and taxo_search(). The filter now uses word boundaries (\bplanet\b) so that genus names containing “planet” as an infix are no longer mistakenly treated as non-biological entries.
• Fixed a lineage parsing bug affecting genera whose Taxonomicon page does not link back to the genus itself (e.g. Periplaneta, which only links to its constituent species). The lineage is now correctly truncated before child species entries, and the genus name is appended if absent.
• Added "Epifamily" to the bare rank token filter so that unprefixed rank labels are not retained as spurious lineage nodes.
• Fixed a lineage parsing bug where the superscript type-marker ᵀ (U+1D40) immediately following a taxon name prevented word-boundary matching in the cutoff search, causing the lineage to overshoot the target node and incorrectly include descendant taxa as ancestors. This silently affected any type genus or type species (i.e. the majority of genera), and was particularly visible in deep clades such as Dinosauria where several child clades were being parsed as ancestor nodes. Higher-rank taxa (clades, orders, families — anything above genus level) were disproportionately affected.
• Fixed a lineage parsing bug where navigation header text prepended to the #divPageContent block could contain the target taxon name (e.g. in a cited reference title), causing the lineage cutoff to land in the junk header rather than the actual taxonomic tree. Affected taxa received a garbage two- or three-line lineage and were silently discarded by the "Biota" membership check in get_taxonomicon_id(). Drosophila (the fly genus, ID 28940) was one such case.

taxodist 0.6.0

Breaking changes

• The distance definition is now a proper ultrametric. Distance is zero only when two complete lineages identify the same hierarchy node. Distinct ancestor-descendant pairs now receive 1 / depth(MRCA) instead of zero. Use is_member() or taxo_path() when the question concerns clade membership or containment rather than distance between nodes.
• Package terminology now consistently describes the measure as a taxonomic hierarchy distance rather than a phylogenetic distance.

Data and documentation

• taxobase is now distributed as a single documented list with provenance metadata, a compact reference distance matrix, and an offline matrix used to build the statistical applications vignette reproducibly.
• Added a methodological vignette defining the distance, demonstrating its ultrametric property, and documenting its assumptions and limitations.
• Revised the introduction and statistical applications vignettes to remove stale hand-written numerical output and distinguish taxonomic dendrograms from inferred phylogenetic trees.
• Added a package citation for taxodist and a separate citation for The Taxonomicon data source.

Bug fixes and robustness

• MRCA detection now uses only the continuous common lineage prefix, preventing repeated names after divergence from being mistaken for shared ancestry.
• is_member() now performs exact, case-insensitive matching and treats regular expression characters literally.
• taxo_path() now correctly handles identical taxa, ancestor-descendant pairs, path direction, lineage depths, and pairs with no common ancestor.
• Empty and single-taxon inputs are handled safely by distance matrices, clustering, ordination, heatmaps, closest-relative queries, and focal distances. Ordination also reduces k when required by sample size.
• Clustering, ordination, and heatmaps now detect NA and infinite distances and return informative fallback objects instead of failing downstream.
• load_cache() validates cache structure, names, and value types before modifying the active cache.

taxodist 0.7.0

Performance

• Optimized distance_matrix() to fill the compact lower-triangular dist representation directly instead of allocating a full square matrix.
• Added a numeric-only pairwise distance path for matrix construction, avoiding allocation of a detailed S3 result object for every taxon pair. Public return values and distance semantics are unchanged.
• Cached the final name-resolved lineage used by distance_matrix(), avoiding repeated filtering and regular-expression work in warm matrix construction.

Compatibility and validation

• Preserved the public API and the continuous-prefix MRCA distance semantics.
• Revalidated the reference matrices and lineage outputs against the Python and Julia implementations.
• Expanded regression coverage for the optimized numeric and cache paths; the package test suite now reports complete source coverage.
• Cache inspection and clearing now address the private cache environment explicitly, avoiding ambiguous search-list lookup during installed use.

taxodist 0.8.0

Auditable name resolution

• Added taxo_resolve() for batch name resolution with explicit resolved, ambiguous, unresolved, and retrieval_error statuses. A missing name is therefore distinguishable from a failed network request or lineage fetch. The result preserves all candidates considered, the selected Taxonomicon ID, the retrieved lineage, and lineage depth for every input.
• Ambiguity handling is now an explicit policy: warn and select the first candidate, select it silently, or stop and require numeric IDs.
• distance_matrix() now accepts a taxodist_resolution object directly, reuses its stored lineages without additional network requests, and keeps the original queried names as matrix labels.
• Added taxo_from_lineages() for curated, unpublished, frozen, or fully offline classifications. User-supplied lineages receive deterministic identifiers and flow through the same matrix and bundle APIs as online resolutions.

Portable analysis bundles

• Added taxo_bundle() to combine resolution records, retrieved lineages, the distance matrix, metric definition, source details, and software metadata in one self-contained object.
• Added write_taxodist_bundle() and read_taxodist_bundle() for a documented JSON format designed for exchange among the R, Python, and Julia implementations.
• Added a bundled JSON Schema for format version 1.0. Missing distances are represented as JSON null, while disconnected infinite distances use the explicit strings "Infinity" and "-Infinity".
• distance_matrix() now also accepts a taxodist_bundle and returns its stored matrix without network access or recomputation.

Robustness and documentation

• Repeated names in taxo_resolve() are now retrieved only once while their original order and repetition are preserved in the audit table.
• Bundle validation now checks resolution fields, candidate counts, selected IDs, lineage depths, matrix labels, and agreement between stored distances and the stored lineages.
• Bundle provenance now supports sources without a URL and preserves custom lineage sources through JSON round trips.
• HTTP requests now report the installed package version in their user agent, and malformed lineage pages fail cleanly instead of escaping as parser errors.
• Reference-data tests now preserve the package version that originally built taxobase instead of requiring it to equal the current development version.
• Corrected stale generated documentation that still used phylogenetic terminology or the pre-0.6 ancestor–descendant distance behavior.

taxodist 0.9.0

Bug fixes

• taxo_resolve() now truncates each selected lineage at the queried taxon exactly as get_lineage() does. Previously it stored the raw lineage of the Taxonomicon page, so for genera whose page does not list the genus itself (e.g. Periplaneta) the lineage stopped at the family, resolved_name reported the family, and distance_matrix(taxo_resolve(x)) could differ from distance_matrix(x). Bundles built from such resolutions inherited the difference.
• Cleaned and uncleaned lineages are now cached separately. Previously, a call to get_lineage_by_id(id, clean = FALSE) was cached under the same key as the cleaned lineage, so later calls with clean = TRUE returned nodes above Biota for the rest of the session. A single request now fills both entries.
• Taxon names are normalized before lookup: surrounding whitespace is removed, repeated spaces are collapsed, and the queried name is matched case-insensitively when truncating the lineage. Previously get_lineage("tyrannosaurus") or get_lineage("Tyrannosaurus ") appended a spurious extra node, inflating the lineage depth, and the distance between "Tyrannosaurus" and "tyrannosaurus" was positive.
• taxo_heatmap() no longer forwards ... to both distance_matrix() and stats::heatmap(). Graphical arguments such as col previously caused an “unused argument” error when taxon names were supplied, and progress produced a graphical-parameter warning. verbose and progress are now explicit arguments.
• cache_info() now reports the names of cached taxa, together with their Taxonomicon IDs in a new ids element. It previously listed only the IDs under taxa.
• get_lineage_by_id() now gives an informative error for a vector of several IDs instead of a low-level coercion error, accepts IDs supplied as numbers, and ignores surrounding whitespace. get_lineage() likewise requires a single name.
• Text scraped from The Taxonomicon is escaped before being included in warnings, so entries containing braces can no longer break the homonym warning.
• Search URLs now percent-encode reserved characters such as &.
• focal_distances() reports the terminal lineage node as the MRCA of a community member identical to the focal taxon, consistently with taxo_distance(), rather than echoing the input name.
• closest_relative() returns consecutive row names after sorting.

Behavior changes

• check_coverage() returns NA when the answer is unknown because The Taxonomicon could not be reached or a candidate lineage could not be retrieved. Previously such names were reported as FALSE, i.e. as absent from the database.
• Validating a bundle when it is printed or passed to distance_matrix() no longer recomputes every distance from the stored lineages; this full integrity check is performed by write_taxodist_bundle() and read_taxodist_bundle(). Printing a bundle of 800 taxa went from about 5 s to under 0.2 s.

Performance

• distance_matrix() now computes distances in vectorized form. Every lineage node is mapped to an integer identifying its complete path from the root, so the MRCA depth of two taxa is the number of depths at which these identifiers agree. For 800 taxa the computation dropped from about 14 s (with the default progress bar) to 0.3 s, with identical results.
• The progress bar of distance_matrix() is updated once per column instead of once per pair; previously it tripled the running time.
• HTTP requests are retried with exponential backoff after network errors and server errors (5xx). The number of attempts is controlled by the new taxodist.max_tries option (default 3).

New features

• taxo_tree() builds an ape-compatible phylo object directly from lineages. Its internal nodes are the named clades at which the taxa diverge, and its branch lengths make the tree ultrametric with patristic distances equal to distance_matrix().
• cross_distances() computes the rectangular matrix of distances between two sets of taxa without computing the full square matrix.
• compare_bundles() reports which taxa changed status, identifier, or lineage between two bundles, and which pairwise distances changed, e.g. when an analysis is repeated after The Taxonomicon is updated. Bundle files can be passed directly by path.
• taxo_resolve() and taxo_bundle() gain a within argument that restricts candidates to a clade (for example within = "Animalia"), resolving many cross-kingdom homonyms automatically.
• save_cache() and load_cache() default to a persistent per-user file in tools::R_user_dir("taxodist", "cache"). save_cache() now returns the written path invisibly.
• distance_matrix(), cross_distances(), and taxo_tree() accept a taxodist_bundle or taxodist_resolution wherever lineages are needed.

Internal changes

• Removed the dependency on purrr and replaced superseded rvest functions (html_nodes(), html_node()) with html_elements() and html_element(). The unused suggested package webmockr was also removed.
• The test suite is split into one file per area (retrieval, resolution, distances, trees, bundles, cache, analysis, and live network tests).
• The parsing of Taxonomicon search pages is shared by get_taxonomicon_id(), taxo_search(), and taxo_resolve().
• The package citation now takes its version from the installed package metadata.
• Tests were extended to cover every new behavior and the package retains complete source coverage.