Inspect a name list for probable typos and other anomalies

A quality-control pass over a name list. By default inspect() does not match names against backbones: on a plain character vector it runs the checks that need no matching – the genus register and the rest of the batch – and is fast and offline. To also surface the match-based anomalies (typo, synonym, ambiguous, geographic), either set backbones = TRUE (matches against every installed backbone, listed in the report) or match yourself first and inspect the result (taxify(x) |> inspect()). Either way it returns only the rows that look anomalous, each labelled with what stands out and, where known, the name to use instead.

Usage

inspect(
  x,
  backbones = FALSE,
  region = NULL,
  coords = NULL,
  range = c("present", "native", "introduced"),
  min_tier = c("note", "review", "unresolved"),
  verbose = TRUE
)

Arguments

x: A character vector of names, or a taxify_result from taxify().
backbones: Logical. When x is a character vector, TRUE matches it against every installed backbone (via taxify()) so the match-based labels are available; FALSE (default) runs the register and list checks only, with no matching. The backbones used are printed in the report header. Ignored when x is already a taxify_result (it was matched already).
region, coords, range: Geographic constraint for the geographic / out_of_range checks, as in taxify(). These act on a taxify_result (which carries the accepted names they need); on a character vector there is nothing matched to place, so they have no effect.
min_tier: Lowest tier to report: "note" (default, everything), "review", or "unresolved".
verbose: Logical. Print progress messages. Default TRUE.

Value

A taxify_inspection data.frame (one row per anomalous name, ordered most-notable first) with columns input_name, suggestion (the name to use instead, or NA), anomalies (|-joined labels), tier (ordered factor note < review < unresolved), reason, fuzzy_dist, and backend. Zero rows means nothing stood out.

Details

Checks that need no matching (run on a character vector or a result):

unknown: The genus is not in the genus register – the union of all 13 backbones' genera – so no backbone recognises it. The strong "probably not a real name" signal.
near_duplicate: A near-twin of a more frequent name in the same list (small edit distance), so probably a misspelling of it. Computed from the list alone, so it catches typos in names no backbone contains.
outlier_group: The name's kingdom group (from the register) is a tiny minority of an otherwise group-coherent list – the lone animal or fungus among plants, typically a cross-kingdom homonym typo.

Checks read from a taxify() result (only present when you inspect one):

typo: Resolved only after fuzzy correction (match_type = "fuzzy"): the input most likely contains a spelling error; suggestion is the name.
ambiguous: A homonym resolving to more than one accepted taxon.
geographic: The matched species is real but has no WCVP record in the declared region / coords (vascular plants only).
out_of_range: No region declared, yet the matched species' range falls outside the list's main TDWG continents (skipped for globally spread lists).
case: Resolved only after ignoring case (match_type = "exact_ci").
synonym: The input is an outdated synonym; suggestion is the current accepted name.

Rows with no anomaly are dropped.

Each row gets a tier describing what it needs, not how bad it is: unresolved (no usable name – act on it), review (a name is there but its identity is uncertain – verify it), or note (correct, optional cleanup). unknown is unresolved; the identity-uncertain labels are review; case and synonym are note. An anomaly may be intended, so the tier is a triage hint, not a verdict.

The list-context labels (near_duplicate, out_of_range, outlier_group) judge a name against the rest of the batch, so they cannot apply to a single name: inspect() on one name warns and reports only the per-name labels. The register checks (unknown, and the register-derived outlier_group) need the genus register installed; without it they are skipped (with a message at verbose).

Examples

old <- options(taxify.data_dir = taxify_example_data())

# On raw names: register + list checks (no matching)
inspect(c("Quercus robur", "Bogusus fakus", "Carexus mysteriosa",
          "Carexus mysteriosa", "Carexus mysteryosa"))

# Opt in to matching to also get typos, synonyms, ambiguity
inspect(c("Quercus robur", "Quercus robus"), backbones = TRUE)

# Or match yourself and inspect the result
taxify(c("Quercus robur", "Quercus robus")) |> inspect()

options(old)