artoo_checks: Control which conformance checks run

In artoo: Lossless CDISC-Native Input and Output for Clinical Datasets

Control which conformance checks run

Description

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,
  invalid_encoding = 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.
invalid_encoding	Flag character values whose bytes are not valid UTF-8. ⁠<logical(1)>: default TRUE⁠. Invalid bytes mean the source was read under a mis-declared encoding; re-read it with the true ⁠encoding=⁠ before the corruption reaches a writer.
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.

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.

Value

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

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()

# ---- 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))

artoo documentation built on July 23, 2026, 1:08 a.m.