td_validate: Check a taxadb table against the taxadb Darwin Core rules
In taxadb: A High-Performance Taxonomic Database Interface

td_validate

R Documentation

Check a taxadb table against the taxadb Darwin Core rules

Description

Check a taxadb table against the taxadb Darwin Core rules

Usage

td_validate(
  provider = getOption("taxadb_default_provider", "itis"),
  schema = c("dwc", "common"),
  version = latest_version(),
  db = td_connect()
)

Arguments

`provider`	from which provider should the hierarchy be returned? Default is 'itis', which can also be configured using `⁠options(default_taxadb_provider=...")⁠`. See `⁠[td_create]⁠` for a list of recognized providers.
`schema`	One of "dwc" (for Darwin Core data) or "common" (for the Common names table.)
`version`	Which version of the taxadb provider database should we use? defaults to latest. See `available_versions()` for details.
`db`	a connection to the taxadb database. See details.

Details

The rules checked are:

columns – the required Darwin Core terms are present, spelled in Darwin Core camelCase.
types – identifier and name columns are character. A column that is entirely NA will often be typed as integer or logical by mistake, which this catches.
scientificName – never NA. Every row names something, at every rank: Animalia is a scientificName just as ⁠Homo sapiens⁠ is.
taxonRank, taxonomicStatus – never NA.
acceptedNameUsageID – never NA, on synonyms and on accepted names. This is where taxadb is stricter than Darwin Core.
accepted_has_id – a row labelled accepted is its own accepted name: taxonID is present and equals acceptedNameUsageID. (taxonID may be NA on a synonym, where the provider mints no identifier for it – OTT and NCBI, for instance, do not.)
accepted_resolves – every acceptedNameUsageID matches the taxonID of a self-referencing row. No dangling references.
synonym_not_self – a row labelled a synonym points somewhere else, never at itself.
taxonID_one_name – a taxonID always names the same scientificName. An identifier may appear on more than one row: ITIS records 255 synonyms that are ambiguous between two accepted taxa, and a row for each is the honest representation. What must not happen is one identifier naming two different names, which is what results from a provider numbering its accepted names and its synonyms in separate sequences and both being given the same prefix.
accepted_unique – no duplicate taxonID among accepted names.
id_prefix – identifiers are the provider's identifier prefixed by the provider abbreviation in capitals, e.g. ITIS:180092.

taxonomicStatus is deliberately not checked against a controlled vocabulary: providers draw real distinctions (⁠homotypic synonym⁠, ⁠provisionally accepted⁠, doubtful, misapplied) that are worth preserving. The rules are therefore phrased structurally. A name the provider does not redirect to another name is its own accepted name whatever confidence it expresses about it, so doubtful and ⁠provisionally accepted⁠ rows self-reference exactly as accepted ones do; only the two terms whose meaning taxadb actually relies on, accepted and synonym, are given a required shape.