Control which conformance checks run

Build a reusable control that selects which dimensions check_spec() evaluates. Construct one per study and thread it through every check_spec() call so the conformance surface is consistent. Each toggle is validated at construction, so a mistyped name or value aborts early rather than being silently ignored.

Usage

artoo_checks(
  missing_variable = TRUE,
  missing_permissible = TRUE,
  extra_variable = TRUE,
  type_mismatch = TRUE,
  length_overflow = TRUE,
  char_length_limit = TRUE,
  codelist_membership = TRUE,
  codelist_membership_extensible = TRUE,
  label_match = TRUE,
  key_uniqueness = TRUE,
  display_format = TRUE,
  variable_name = TRUE,
  dataset_name = TRUE,
  label_length = TRUE,
  integer_overflow = TRUE,
  integer_fraction = TRUE,
  iso8601_format = TRUE
)

Arguments

missing_variable

Flag mandatory spec variables absent from the data. <logical(1)>: default TRUE.

missing_permissible

Flag permissible (non-mandatory) spec variables absent from the data. <logical(1)>: default TRUE.

extra_variable

Flag data columns the spec does not declare. <logical(1)>: default TRUE.

type_mismatch

Flag columns whose storage differs from the spec dataType. <logical(1)>: default TRUE.

length_overflow

Flag character values longer than the spec length. <logical(1)>: default TRUE.

char_length_limit

Flag character values longer than the SAS XPORT v5 / FDA 200-byte limit. <logical(1)>: default TRUE.

codelist_membership

Flag values outside their closed codelist. <logical(1)>: default TRUE.

codelist_membership_extensible

Flag values outside an extensible codelist's enumerated terms. <logical(1)>: default TRUE. A codelist whose extended flag is TRUE allows sponsor terms, so a non-member is a note, never an error; this toggle silences those notes independently of codelist_membership.

label_match

Flag a column whose label attribute differs from the spec label. <logical(1)>: default TRUE.

key_uniqueness

Flag a dataset whose spec key variables do not uniquely identify its rows. <logical(1)>: default TRUE.

display_format

Flag a date/datetime/time variable whose displayFormat is not a recognized SAS format of that family. <logical(1)>: default TRUE.

variable_name

Flag a data column name that violates the XPORT naming rules. <logical(1)>: default TRUE. Over 8 characters (the v5 limit), over 32 (the v8 limit), or containing anything but ASCII letters, digits, and underscore.

dataset_name

Flag a dataset name that violates the XPORT naming rules. <logical(1)>: default TRUE. Same limits as variable_name.

label_length

Flag a column label attribute over the 40-byte XPORT v5 / FDA limit. <logical(1)>: default TRUE.

integer_overflow

Flag an integer-typed variable holding values beyond R's 32-bit integer range. <logical(1)>: default TRUE. Such values become NA under coercion, so this is an error, not a warning.

integer_fraction

Flag an integer-typed variable holding fractional values. <logical(1)>: default TRUE. Coercion would truncate them (162.6 becomes 162) — a data-integrity event; fix the spec dataType (float / decimal) or the data before conforming.

iso8601_format

Flag a character date/datetime/time variable whose values are not valid ISO 8601 text. <logical(1)>: default TRUE. A character column under a temporal dataType is the CDISC --DTC form; complete values, right-truncated partials ("1951", "1951-12"), and SDTMIG hyphen placeholders ("2003---15") all pass, while "12NOV2019" or an impossible calendar date is flagged.

Value

A <artoo_checks> control object. Pass it as the checks argument to check_spec().

Details

Selection, not severity. This control decides which findings are produced; apply_spec()'s conformance argument (warn, abort, off) decides what to do with the findings its full-default check raises. A disabled dimension is skipped entirely, so the findings frame stays clean.

See also

check_spec(), which consumes it; apply_spec() for the findings disposition.

Examples

# ---- Example 1: the default runs every conformance dimension ----
#
# With no arguments, every conformance dimension is enabled.
artoo_checks()
#> <artoo_checks>
#>   [x] missing_variable
#>   [x] missing_permissible
#>   [x] extra_variable
#>   [x] type_mismatch
#>   [x] length_overflow
#>   [x] char_length_limit
#>   [x] codelist_membership
#>   [x] codelist_membership_extensible
#>   [x] label_match
#>   [x] key_uniqueness
#>   [x] display_format
#>   [x] variable_name
#>   [x] dataset_name
#>   [x] label_length
#>   [x] integer_overflow
#>   [x] integer_fraction
#>   [x] iso8601_format

# ---- Example 2: silence one dimension for a whole study ----
#
# Turn off the length check (e.g. while a spec's lengths are provisional)
# and reuse the control across every dataset.
spec <- artoo_spec(cdisc_sdtm_datasets, cdisc_sdtm_variables, codelists = cdisc_codelists)
ck <- artoo_checks(length_overflow = FALSE)
nrow(check_spec(cdisc_dm, spec, "DM", checks = ck))
#> [1] 0