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Export a recipe population to an OHDSI Circe cohort expression

Source: R/recipe.R
recipe_export_circe.Rd

Maps the recipe POPULATION / cohort layer to an OHDSI Circe cohort-expression JSON (the format ATLAS imports/exports). The entry event comes only from an explicit omop_index_event. This is an executable, fail-closed subset: unsupported semantics raise an error rather than being omitted and accidentally broadening the cohort.

Usage

recipe_export_circe(recipe, population_id = "base", file = NULL)

Arguments

recipe

An omop_recipe object.

population_id

Character; which population to export (default "base").

file

Character or NULL; path to write the Circe JSON to. If NULL, the JSON string is returned.

Value

The Circe JSON string (if file is NULL) or the file path invisibly.

Details

Supported constructs (recipe <-> Circe):

  • omop_index_event on a condition/drug/measurement/observation/ procedure/device/visit table -> PrimaryCriteria First/Last. Direct dsOMOP plans also support All; Circe All is rejected because Circe subsequently applies ERA collapse while dsOMOP preserves individual episodes.

  • omop_filter_has_concept -> InclusionRule occurrence criteria; it is never implicitly promoted to an entry event.

  • omop_filter_not_has_concept -> InclusionRule occurrence "exactly 0" criteria.

  • omop_filter_concept_count -> InclusionRule occurrence "at least N" criteria.

  • Presence-only omop_filter_has_measurement -> Measurement criteria. Numeric bounds are rejected because Circe cannot carry the DataSHIELD-issued safe-bin contract.

  • omop_filter_sex / omop_filter_age -> DemographicCriteria Gender / Age.

  • Filter window = list(start, end) day offsets -> criteria StartWindow (index-relative days).

  • omop_filter_prior_observation / omop_filter_followup -> the entry event ObservationWindow (PriorDays / PostDays).

  • An explicit OHDSI DateOffset end strategy (StartDate or EndDate plus an integer offset) -> EndStrategy. With no strategy, cohort exit defaults to the covering observation-period end.

  • An omop_filter_group(operator = "OR") -> a nested Circe CriteriaGroup of Type ANY; the population's top-level AND criteria map to the cohort's implicit ALL.

Intentionally unsupported (rejected, never silently lost): set-operation populations, cohort_definition_id references, fixed-reference ages/windows, age_group, visit_count, missing_measurement, value_bin / value_concept / date_range (row-level) filters, and the recipe variable/output layer. Circe end strategies other than DateOffset, censoring strategies, non-start windows, unsupported occurrence operators, multiple primary criteria, and nested groups are rejected on import.

See also

recipe_import_circe, omop_population

Examples

if (FALSE) { # \dontrun{
recipe <- omop_recipe(
  populations = omop_population(
    id = "t2d", label = "Type 2 diabetes, female, 18-65",
    index_event = omop_index_event(201820, "condition_occurrence"),
    filters = list(
      omop_filter_sex("F"),
      omop_filter_age(18, 65))),
  outputs = omop_output(type = "wide", population_id = "t2d"))
circe_json <- recipe_export_circe(recipe, population_id = "t2d")
# Imports the executable supported subset:
pop <- recipe_import_circe(circe_json)
} # }