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Check taxonID

Source: R/dct_check_taxon_id.R
dct_check_taxon_id.Rd

Check for correctly formatted taxonID column in Darwin Core taxonomic data.

Usage

dct_check_taxon_id(
  tax_dat,
  on_fail = dct_options()$on_fail,
  on_success = dct_options()$on_success,
  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".

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:

  • taxonID may not be missing (NA)

  • taxonID must be unique

Examples

dct_check_taxon_id(
  data.frame(taxonID = NA_character_),
  on_fail = "summary", quiet = TRUE
)
#> # A tibble: 1 × 3
#>   taxonID error                               check         
#>   <chr>   <chr>                               <chr>         
#> 1 NA      taxonID detected with missing value check_taxon_id
dct_check_taxon_id(data.frame(taxonID = 1))
#>   taxonID
#> 1       1