Stage 5: run numeric, unit, media, and ToxVal harmonization

Usage

stage_harmonize(
  state,
  harmonize = FALSE,
  unit_map = NULL,
  unit_map_snapshot = NULL,
  corrections = NULL,
  media_map = NULL,
  media_map_snapshot = NULL,
  media = NULL,
  source_name = NULL,
  toxval_identity_mode = c("lookup", "accepted")
)

Arguments

state: State list from stage_review().
harmonize: Logical. If TRUE, runs numeric parsing, unit harmonization, and ToxVal schema mapping after curation. Default FALSE for backward compat.
unit_map: Tibble with unit conversion mappings, or NULL (default) to load from package cache via load_unit_map().
unit_map_snapshot: Optional compact replay snapshot from generate_concert_script(); reconstructs the effective unit map from package defaults plus embedded deltas. Mutually exclusive with unit_map.
corrections: Tibble with pattern/replacement columns for one-off corrections, or NULL (default) to load from package cache.
media_map: Optional media harmonization map passed to harmonize_media().
media_map_snapshot: Optional compact replay snapshot from generate_concert_script(); reconstructs the effective media map from package defaults plus embedded deltas. Mutually exclusive with media_map.
media: Character. Media context for ppb/ppm routing: "aqueous", "air", or "solid". NULL (default) uses aqueous assumption.
source_name: Optional dataset identifier for ToxVal source. Defaults to the input filename stem.
toxval_identity_mode: ToxVal identifier policy: "lookup" preserves the existing audit export default; "accepted" gates IDs and preserves every measurement row with NA IDs when blocked.

Value

The state with harmonize, harmonization_refs, harmonization_runtime_result, toxval_output, harmonize_audit, and detection_results added. When harmonize = FALSE, the harmonization flag and identity policy are retained.