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Check mapping of usage taxonomic IDs

Source: R/dct_check_mapping.R
dct_check_mapping.Rd

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.

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

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.

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)
#> # A tibble: 1 × 5
#>   taxonID acceptedNameUsageID scientificName error                         check
#>   <chr>   <chr>               <chr>          <glue>                        <chr>
#> 1 3       4                   Species bat    taxonID detected whose accep… chec…