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.