dct_check_mapping: Check mapping of usage taxonomic IDs

In dwctaxon: Edit and Validate Darwin Core Taxon Data

Check mapping of usage taxonomic IDs

Description

Check that values of terms like 'acceptedUsageID' map properly to taxonID in Darwin Core (DwC) taxonomic data.

Usage

dct_check_mapping(
  tax_dat,
  on_fail = dct_options()$on_fail,
  on_success = dct_options()$on_success,
  col_select = "acceptedNameUsageID",
  quiet = dct_options()$quiet
)

Arguments

tax_dat	Dataframe; taxonomic database in DwC format.
on_fail	Character vector of length 1, either "error" or "summary". Describes what to do if the check fails. Default "error".
on_success	Character vector of length 1, either "logical" or "data". Describes what to do if the check passes. Default "data".
col_select	Character vector of length 1; the name of the column (DwC term) to check. Default "acceptedNameUsageID".
quiet	Logical vector of length 1; should warnings be silenced? Default FALSE.

Details

The following rules are enforced:

• Value of taxonID may not be identical to that of the selected column within a single row (in other words, a name cannot be its own accepted name, parent taxon, or basionym).

• Every value in the selected column must have a corresponding taxonID.

col_select can take one of the following values:

• "acceptedNameUsageID": taxonID corresponding to the accepted name (of a synonym).

• "parentNameUsageID": taxonID corresponding to the immediate parent taxon of a name (for example, for a species, this would be the genus).

• "originalNameUsageID": taxonID corresponding to the basionym of a name.

Value

Depends on the result of the check and on values of on_fail and on_success:

• If the check passes and on_success is "logical", return TRUE

• If the check passes and on_success is "data", return the input dataframe

• If the check fails and on_fail is "error", return an error

• If the check fails and on_fail is "summary", issue a warning and return a dataframe with a summary of the reasons for failure

Examples

# The bad data has an acceptedNameUsageID (third row, "4") that lacks a
# corresponding taxonID
bad_dat <- tibble::tribble(
  ~taxonID, ~acceptedNameUsageID, ~taxonomicStatus, ~scientificName,
  "1", NA, "accepted", "Species foo",
  "2", "1", "synonym", "Species bar",
  "3", "4", "synonym", "Species bat"
)

dct_check_mapping(bad_dat, on_fail = "summary", quiet = TRUE)

dwctaxon documentation built on May 29, 2024, 5:53 a.m.