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Match taxonomic names against local backbone databases

Source: R/taxify.R
taxify.Rd

Matches a vector of taxonomic names against locally stored Darwin Core backbone databases. Returns a data.frame with one row per input name containing the matched name, accepted name, taxonomic hierarchy, and match quality information.

Usage

taxify(
  x,
  backbone = NULL,
  fuzzy = TRUE,
  fuzzy_threshold = 0.2,
  fuzzy_method = c("dl", "levenshtein", "jw"),
  aggregates = c("preserve", "collapse"),
  region = NULL,
  coords = NULL,
  range = c("present", "native", "introduced"),
  kingdom = NULL,
  mode = c("fallback", "wide", "agreement"),
  verbose = TRUE
)

Arguments

x

Character vector of taxonomic names.

backbone

Character vector of backbone names (e.g., "wfo", "col", "gbif") or a single taxify_backend object. Several are tried in order as a fallback chain. NULL (default) uses every installed backbone in priority order, installing the default set (COL, GBIF, ITIS) on first use; override the priority with options(taxify.backbone_priority = ...) and the first-run set with options(taxify.default_backbones = ...).

fuzzy

Logical. Enable fuzzy matching for names that fail exact match. Default TRUE.

fuzzy_threshold

Numeric. Maximum allowed distance for fuzzy matches. Two modes depending on the value:

  • Fractional (0 < fuzzy_threshold < 1): normalized distance (edits / max name length). Default 0.2 is about 1 edit per 5 characters.

  • Integer (fuzzy_threshold >= 1): maximum raw edit count, e.g. fuzzy_threshold = 2L allows at most 2 insertions/deletions/substitutions regardless of name length. Not supported for fuzzy_method = "jw".

fuzzy_method

Character. One of "dl" (Damerau-Levenshtein, default), "levenshtein", or "jw" (Jaro-Winkler).

aggregates

Character. How to treat species aggregates (names with an agg. / s.l. qualifier). "preserve" (default) keeps the aggregate as its own concept: it matches the backbone's aggregate taxon ("<binomial> aggr.") where one exists, otherwise falls back to the binomial. The output's aggregate_fallback column records which happened for each aggregate: TRUE where it fell back to the binomial, FALSE where it resolved to the dedicated aggregate taxon. Only Euro+Med and WoRMS carry aggregate taxa, so preserve falls back for the other backbones. "collapse" strips the marker and matches the binomial species, the way any non-aggregate name is matched. Either way the qualifier is recorded in the qualifier column.

region

Region(s) to constrain fuzzy matching to, or NULL (default) for no geographic constraint. Botanical (WCVP, vascular plants): TDWG Level 3 codes ("BGM", c("BGM", "GER")) or region names at any level, matched case- and accent-insensitively against the bundled WGSRPD crosswalk – a Level 3 name ("Belgium"), a Level 2 region ("Middle Europe"), or a Level 1 continent ("Europe", which expands to all its codes). Marine (only when the marine_distribution asset is installed): a MEOW ecoregion ECO_CODE, or an ecoregion / province / realm name (a province or realm expands to its member ecoregions). See taxify_regions() for both lists. When set, fuzzy candidates are restricted to species with range records in the region(s); exact matches are always kept. The filter only narrows genuinely ambiguous fuzzy candidates: a candidate is dropped only when the same input name has another candidate that is in-region or has no range data, so a match in a group with no range coverage is never affected and a name whose only candidate is out-of-region is still returned.

coords

Coordinates to constrain fuzzy matching to, mapped to region codes by point-in-polygon and unioned with region. Points are tested against the WGSRPD botanical boundaries (yielding TDWG codes) and, when the marine asset is installed, the MEOW ecoregion boundaries (yielding ECO_CODEs), so a coastal point can resolve to both. A single c(lon, lat) pair, a matrix/data.frame of longitude/latitude columns (named lon/lat or x/y, else the first two columns as lon, lat), or a point-geometry spatial object (an sf/sfc object or a terra SpatVector, reprojected to longitude/latitude automatically). NULL (default) for none. Each boundary file is downloaded once and cached; coordinate lookup needs that download (or a prior cache). The point-in- polygon test uses terra or sf when installed, otherwise a native fallback; force the engine with options(taxify.pip_engine = "terra" | "sf" | "native").

range

Character. Which range statuses count as in-region when region or coords is set. "present" (default) accepts any record (native, introduced, extinct, or unknown status) – the right choice for name disambiguation. "native" accepts only native records, "introduced" only introduced (alien) records; both fold an ecological filter into matching and are for callers who want that. Ignored when no region is set.

kingdom

Character. Restrict matches to one or more kingdoms, to disambiguate a name shared across kingdoms (a Prunella that is both a bird and a plant, an Oenanthe that is both). NULL (default) applies no constraint. Accepts a kingdom name or a common alias, case-insensitively: "animals"/"Animalia"/"Metazoa", "plants"/"Plantae", "fungi", "bacteria", "archaea", "chromista", "protozoa", "viruses". A matched taxon is kept only when its kingdom is the requested one (or is unknown, which is never rejected); with the default multi-backbone fallback, a name a backbone resolves into the wrong kingdom is passed on to the next backbone, so the in-kingdom treatment wins. The kingdom is read from the backbone where it stores one (COL, ITIS, NCBI, OTT, WoRMS); for a backbone that does not (WFO, GBIF), it falls back to the genus register's kingdom, which cannot split a genus that is itself homonymous across kingdoms – name a kingdom-appropriate backbone for those.

mode

Character. How to combine results when backbone names more than one backbone. "fallback" (default) is the fallback chain described above: one answer per name, from the first backbone that matched. "wide" and "agreement" instead consult every backbone for every name and report how they compare, so a backbone disagreement (see the Backbone-specific accepted names section) is visible in one call rather than by querying each backbone by hand. Both return a strict superset of the "fallback" result (the same standard columns, with accepted_name still the fallback pick, so the frame still pipes into the add_*() enrichments) plus:

  • "wide": one accepted_<backbone> column per backbone and a logical all_agree.

  • "agreement": n_backbones_matched, n_distinct_accepted, and all_agree.

all_agree is TRUE/FALSE when at least two backbones matched the name and NA when fewer than two did (nothing to compare). Ignored (with a message) when only one backbone is given, since there is nothing to compare.

verbose

Logical. Print progress messages. Default TRUE.

Value

A data.frame with one row per input name and the following columns:

input_name

The original name as provided.

matched_name

Full name in the backbone that matched. For an unresolved hybrid formula (match_type = "hybrid_formula") it holds the input-parent cross (e.g. "Salix alba x Salix fragilis") when both parents resolve, else NA.

accepted_name

Resolved accepted name (equals matched_name if not a synonym). For a hybrid formula it holds the accepted-parent cross (both parents resolved), else NA.

taxon_id

Backend-specific ID of the matched name.

accepted_id

ID of the accepted name.

rank

Taxonomic rank (species, subspecies, genus, etc.).

family

Family name.

genus

Genus name.

epithet

Specific epithet.

authorship

Authorship of the matched name.

accepted_authorship

Authorship of the accepted name. For a synonym this is the author of the resolved accepted name, not the synonym's own author, so accepted_name and accepted_authorship together form the accepted name's full citation.

is_synonym

Logical. Was the match a synonym?

is_hybrid

Logical. Was a hybrid marker detected in the input?

hybrid_type

"nothogenus" ("x Cupressocyparis leylandii"), "nothospecies" ("Quercus x hispanica"), "formula" ("Salix alba x Salix fragilis"), or NA for a non-hybrid. Nothogenus and nothospecies resolve to a single backbone taxon in the usual columns. A formula resolves that way only where the backbone stores the cross; otherwise match_type is "hybrid_formula", the ID, rank and classification columns are NA, and matched_name / accepted_name name the cross by its parents when both parents resolve. The parent binomials, and their accepted names, are added on demand by add_hybrid_info().

qualifier

Canonical taxonomic qualifier found in the input name ("cf.", "aff.", "agg.", "s.l.", "s.str.", "sp.", ...), or NA. Spelling variants are folded to one token ("aggr.", "agg" and "sensu lato" all map to "agg."/"s.l.").

qualifier_position

"genus" when the qualifier leads the name and qualifies the whole name (e.g. "Cf. Pinus sylvestris"), "species" when it qualifies the species (inline cf. or trailing agg.), NA when there is no qualifier.

aggregate_fallback

Logical. For an aggregate query under aggregates = "preserve": FALSE when it resolved to the backbone's dedicated aggregate taxon, TRUE when no such taxon existed and it fell back to the nominal binomial. NA for non-aggregate queries and under aggregates = "collapse", where the collapse is explicit.

match_type

One of "exact", "exact_ci", "fuzzy", "abbrev" (an abbreviated genus such as "Q. robur" resolved via genus initial plus epithet), "hybrid_formula" (a two-parent cross the backbone does not store; the ID, rank and classification columns are NA, matched_name / accepted_name name the cross by its parents when both resolve, and add_hybrid_info() materializes the parents into the hybrid_parent_* columns), or "none".

fuzzy_dist

Normalized string distance (0–1), NA if exact.

is_ambiguous

Logical. TRUE when the matched scientificName had multiple synonym rows pointing to different accepted taxa at the same priority tier (homonym ambiguity). Disambiguated via nomenclaturalStatus = "Valid" when that column is in the backbone; for irreducible ambiguity, the scalar columns hold one candidate.

ambiguous_targets

Character. |-joined list of conflicting accepted taxon IDs when is_ambiguous = TRUE; NA otherwise.

backbone

Which backbone was used (e.g., "wfo", "col", "gbif").

backbone_version

Backend name, version, and download date (e.g., "wfo:2024-12 (2026-04-01)"). Useful for reproducibility.

kingdom_group

Coarse kingdom-level group of the matched genus, from the bundled genus register (used for cross-kingdom disambiguation); NA when the genus is not in the register.

taxon_group

Broad taxonomic group of the matched genus, from the genus register; NA when unavailable.

life_form

Life-form classification of the matched genus, from the genus register's family-based lookup; NA when unavailable.

Details

By default taxify() matches against every installed backbone, tried in priority order as a fallback chain (the COL syntheses, then the domain authorities, then the broad aggregators). The chain is staged by match quality: every backbone is asked for an exact match first, and only the names still unresolved go round again for a fuzzy one. A name is therefore resolved by the highest-priority backbone that matches it at the best quality any backbone reaches, so a near neighbour in an early backbone does not settle a name a later backbone holds exactly. Names matched earlier are not re-matched later. On a fresh setup with nothing installed yet, the first call downloads a default set (COL, GBIF, ITIS) once; pre-install a different set with install_backbones(). Name a backbone (or several) explicitly to match only against that one, or those in that order.

Backbone-specific accepted names

Each backbone is an independent taxonomy, and they can legitimately disagree on which name is accepted and which is a synonym. taxify() returns the matched backbone's own current treatment; it does not reconcile backbones against each other by voting (a consensus would regress toward the most conservative treatment across backbones that copy one another). With the default multi-backbone fallback, accepted_name is the pick of the highest-priority backbone that matched at the best quality reached. To see where backbones disagree, pass mode = "wide" (or "agreement") for each backbone's accepted_name side by side; to follow one authority, name a single backbone.

For example, the red and parma kangaroos: the GBIF Backbone Taxonomy accepts Macropus rufus and Macropus parma, treating Osphranter rufus and Notamacropus parma as synonyms of them, so taxify("Osphranter rufus", backbone = "gbif") resolves to Macropus rufus. The Catalogue of Life splits the genus and does the reverse, so taxify("Macropus rufus", backbone = "col") resolves to Osphranter rufus. Both are faithful to their source; the difference is in the backbones, not in the matching.

Examples

# Runs offline against the bundled example database.
old <- options(taxify.data_dir = taxify_example_data())

# Match a few names
taxify(c("Quercus robur", "Pinus sylvestris"))

# Disable fuzzy matching
taxify("Quercus robus", fuzzy = FALSE)

# Constrain fuzzy candidates to a geographic region: a TDWG Level 3 code,
# or a region name resolved via the bundled WGSRPD crosswalk
taxify("Quercus robus", region = "EUR")
taxify("Quercus robus", region = "Belgium")

# Constrain by coordinates (downloads WGSRPD boundaries on first use)
if (FALSE) { # \dontrun{
taxify("Quercus robus", coords = c(4.35, 50.85))
} # }

# Fallback chain: try WFO first, then COL for unmatched
taxify(c("Quercus robur", "Panthera leo"),
       backbone = c("wfo", "col"))

# Compare how two backbones resolve the same names, side by side
taxify(c("Quercus robur", "Pinus sylvestris"),
       backbone = c("wfo", "col"), mode = "wide")

options(old)