High-Performance Open-Source Archive
taxo_distance(), mrca(),
distance_matrix(), closest_relative(),
compare_lineages(), shared_clades(),
is_member(), filter_clade(),
lineage_depth(), check_coverage(),
clear_cache()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.Statistical Applications of taxodist) demonstrating the
integration of taxodist with ape (tree
plotting) and vegan (taxonomic distinctness, Mantel tests,
and PERMANOVA).vegan to Suggests in
DESCRIPTION.distance_matrix()
output with vegan functions (taxondive(),
mantel(), adonis2()).taxo_cluster() results
into phylo objects using ape::as.phylo().[crown]) being matched across different lineages as if
they were the same ancestor.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).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.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.Subgenus, Section, Division,
Subdivision, Supercohort,
Infracohort, Subsection,
Candidatus, Parvphylum, Branch,
and Go to (a navigation artefact from The Taxonomicon page
layout).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.Bacteria), the warning now lists all available
numeric IDs without duplicates, allowing users to make an informed
choice.organisms) appearing
before Biota.get_lineage_by_id() to silently
return NULL for non-numeric strings, preventing upstream
server fallback errors.Genus
was erroneously truncated from species-level queries. Distances and Most
Recent Common Ancestors (MRCAs) between congeneric species are now
computed accurately."Redtenbacher, 1906") were evading the
lineage cleaning pipeline and being erroneously retained as part of the
clade name.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.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.auct. author annotations (e.g.,
Subphylum Craniata auct.) that were preventing
rank-prefixed names from being correctly cleaned.Romeriida Gauthier,). The author removal pipeline now
handles these patterns correctly.†)
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.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.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."Epifamily" to the bare rank token filter so that
unprefixed rank labels are not retained as spurious lineage nodes.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.#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.
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