repair_spec: Repair a spec from its conformance findings

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

Repair a spec from its conformance findings

Description

Take the integer_fraction and integer_overflow findings a check_spec() or check_study() run reports and return a new spec with every offending variable retyped to "float", so a frame that the original spec would refuse to coerce now conforms. This closes the loop on the spec-side fix: inspect the findings, then apply them all at once instead of editing the source workbook variable by variable. Persist the result with write_spec().

Usage

repair_spec(spec, findings)

Arguments

spec	The specification to repair. ⁠<artoo_spec>: required⁠.
findings	A findings data frame. ⁠<data.frame>: required⁠. The result of check_spec() or check_study(); must carry the check, dataset, and variable columns.

Details

Scope. Only the two lossy-integer findings are repaired (integer_fraction, integer_overflow) — both mean "the spec says integer but the data is not", and "float" is the loss-free fix. Other findings are ignored; this is not a general spec rewriter. When no repairable finding is present the spec is returned unchanged, with a note.

Built on set_type(). Each ⁠(dataset, variable)⁠ pair is applied through the same validated override set_type() uses, so the result is a fully re-validated artoo_spec, never a hand-edited internal.

Value

A new ⁠<artoo_spec>⁠ with the flagged variables retyped to "float", or spec unchanged when there is nothing to repair. The input is never mutated.

See Also

Primitive: set_type() to retype a chosen variable directly.

Findings: check_spec() for one dataset, check_study() across a study. Persist: write_spec().

Examples

# ---- Example 1: auto-repair an integer/fractional mismatch ----
#
# adam_spec types ADSL.AGE as integer. Give it fractional ages and
# check_spec() raises an integer_fraction error; repair_spec() flips AGE
# (and only AGE) to float, and the corrected spec then applies cleanly.
dat <- cdisc_adsl
dat$AGE <- dat$AGE + 0.5
findings <- check_spec(dat, adam_spec, "ADSL")
fixed <- repair_spec(adam_spec, findings)
spec_variables(fixed, "ADSL")$data_type[
  spec_variables(fixed, "ADSL")$variable == "AGE"
]

# ---- Example 2: nothing to repair is a no-op ----
#
# The bundled data conforms, so its findings carry no integer_fraction or
# integer_overflow rows and the spec is returned unchanged.
clean <- check_spec(cdisc_adsl, adam_spec, "ADSL")
identical(repair_spec(adam_spec, clean), adam_spec)

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