taxify_data_dir() can now be redirected with the
taxify.data_dir option or the TAXIFY_DATA_DIR
environment variable, so the cache location is configurable (shared
caches, scratch directories, the bundled example data).taxify_example_data() returns the path to a small
bundled example database (a handful of species per backbone plus
matching enrichment tables). Setting
options(taxify.data_dir = taxify_example_data()) lets
matching and enrichment run fully offline.\dontrun{}. Only
add_pignatti() (fetched live via TR8) and
list_enrichments() (reads the online manifest) remain in
\donttest{}.add_floraweb() joins German-flora plant traits from
FloraWeb (the live BfN portal carrying the BiolFlor data of Klotz, Kuehn
& Durka 2002, plus Rothmaler morphology and Ellenberg indicator
values). It bundles the full per-species trait profile – morphology,
reproductive biology, the nine Ellenberg indicator values, ploidy and
chromosome number, and chorological distribution (59 _de
columns) – as a pre-built dataset, so it works offline.add_ecoflora() now joins a bundled, pre-built
Ecoflora dataset (18 _uk columns: canopy height, leaf
traits, life form, flowering phenology, pollination, seed weight, and
British-calibrated Ellenberg values) instead of fetching live through
TR8. It works offline and returns the full trait set rather than the
previous five columns.
add_pignatti() remains an on-demand TR8 source: its
values are from a copyrighted publication and cannot be
redistributed.
add_ecoflora(), add_biolflor(), and
add_pignatti() join plant traits that taxify does not ship
as a pre-built dataset, accessing them on demand through the suggested
TR8 package on your own machine; taxify redistributes nothing. The
reasons differ by source: add_ecoflora() adds British
flowering months, pollen vector, life form, and leaf longevity (CC
BY-NC-SA, which would allow redistribution, but ecoflora.org.uk has no
bulk download, so it is fetched live per species);
add_biolflor() adds Grime CSR strategy type, breeding
system, pollen vector, life form, life span, and apomixis (usable with
acknowledgement + citation per the BioFresh metadata statement, but no
bulk copy is obtainable while the UFZ site is offline, so fetched live);
add_pignatti() adds Italian Ellenberg-type indicator
values, life form, and chorotype (copyrighted; read from the copy
bundled in TR8, which TR8 redistributes, not taxify; works offline).
Columns are region-suffixed
(_uk/_de/_it) so they never
collide with add_baseflor(). TR8 is a Suggests dependency.
If a live source (Ecoflora, BiolFlor) is unreachable the call errors
rather than attaching silent NA.add_baseflor() joins plant traits from Baseflor
(Programme Catminat, Julve 1998 ff.; ODbL 1.0 / CC BY-SA 2.0) to a
taxify() result. It covers ~7,000 vascular plant taxa of
France and neighbouring regions and adds flowering phenology
(flower_begin_month, flower_end_month),
pollination vector, dispersal mode, breeding system, flower colour,
fruit type, woody growth form, and the continentality and salinity
indicator-value axes absent from EIVE. The enrichment is registered in
the manifest (list_enrichments()) with a pre-built
.vtr; light/temperature/moisture/reaction/nutrient axes are
left to add_eive() and Raunkiaer life form to
add_leda().tests/e2e/test-e2e-enrichment.R) for the enrichment join
fixed in 0.2.5 (#1). It checks that
add_conservation_status(), add_common_names(),
and add_woodiness() attach each value to the row’s own
accepted taxon, stay invariant to batch composition and order, and land
documented values on the correct species."Q. robur" now resolve.
A matching pass restricts the backbone to rows whose genus starts with
the given initial and whose specific epithet matches, resolving only
when that is unique. When two or more genera sharing the initial also
share the epithet the abbreviation is ambiguous: the row is left
unmatched with is_ambiguous = TRUE and the conflicting
accepted IDs in ambiguous_targets, rather than guessing a
genus. A genus spelled out in full elsewhere in the same input takes
precedence (the convention of abbreviating after first mention).
Resolved rows carry match_type = "abbrev".accepted_authorship output column: the authorship
of the resolved accepted name. For a synonym match,
authorship holds the synonym’s own author while
accepted_authorship holds the accepted name’s author, so
accepted_name and accepted_authorship together
form the accepted taxon’s full citation. Backbones that carry authorship
populate it; sources without authorship (NCBI, OTT) return
NA.taxify() no longer errors with “replacement has length
zero” for backbones whose .meta sidecar records the build
date as build_date (the current taxifydb build format)
rather than download_date. Backbone metadata now reads both
layouts and version formatting tolerates a missing date. This previously
broke matching against the WoRMS and Open Tree of Life backbones.Additional_repositories (https://gcol33.r-universe.dev), so
its location is discoverable as required for a Suggests dependency
outside the mainstream repositories.taxify() no longer errors with “incorrect number of
dimensions” when the genus register is present but the backend-coverage
file is not (the state on a clean install before any coverage download,
and during package checks). An early return() evaluated
inside a tryCatch() expression returned NULL
from the pre-filter, which $<- then turned into a list;
the out-of-scope pre-filter now resolves missing coverage to a no-op and
preserves the result data frame.
Replaced non-ASCII characters in roxygen documentation with ASCII equivalents so the PDF reference manual builds under LaTeX.
Ambiguous homonym synonyms now resolve to the epithet-preserving
accepted name (the homotypic basionym) instead of an arbitrary lowest-id
candidate. taxify("Pinus abies") resolves to Picea
abies (not Picea polita), and the spurious
is_ambiguous flag is cleared when one candidate keeps the
specific epithet (#2). Genuinely ambiguous names (no candidate, or
several, preserving the epithet) are still flagged.
Silenced tidyselect deprecation warnings emitted during fuzzy matching.
score_candidates() is exported (kept internal in the
reference index) so the companion taxifydb build pipeline
can collapse each backbone key to the single accepted name
taxify() resolves it to. This corrects enrichment joins
that previously landed trait/status values on within-genus neighbours
(#1); the fix reaches users through rebuilt enrichment data.
Need a high-speed mirror for your open-source project?
Contact our mirror admin team at info@clientvps.com.
This archive is provided as a free public service to the community.
Proudly supported by infrastructure from VPSPulse , RxServers , BuyNumber , UnitVPS , OffshoreName and secure payment technology by ArionPay.