generate_concept_cohort_set

generate_concept_cohort_set(
    cdm,
    concept_set,
    *,
    name='cohort',
    limit='first',
    required_observation=(0, 0),
    end='observation_period_end_date',
    subset_cohort=None,
    subset_cohort_id=None,
    overwrite=True,
)

Generate a cohort set from one or more concept sets (named list of concept IDs).

Each concept set becomes one cohort; each row represents the time during which the concept was observed for that subject. Concepts are looked up in the CDM vocabulary and domain tables (condition_occurrence, drug_exposure, etc.). Concepts not in the vocabulary or in missing domain tables are silently skipped. If a domain has no end date (e.g. procedure, observation), start date is used as end date.

Parameters

Name	Type	Description	Default
cdm	Cdm reference (from cdm_from_con with observation_period and concept table).		required
concept_set	dict[str, list[int] | list[dict]]	Named concept sets: name -> list of concept_id (int) or list of concept specs (dict). Each name becomes one cohort. Concept specs are dicts with: - “concept_id” (int, required) - “include_descendants” (bool, optional): if True, expand via concept_ancestor (requires concept_ancestor table). Default False. - “is_excluded” (bool, optional): if True, exclude this concept from the set. Default False. Simple form: {“cohort_a”: [192671, 123]} uses no descendants and not excluded.	required
name	str	Name of the cohort table (lowercase, letters/numbers/underscores). Default “cohort”.	'cohort'
limit	str	“first” (default) or “all”: include only first occurrence per subject per cohort, or all.	'first'
required_observation	tuple[int, int]	(prior_days, future_days) required observation around the event. Default (0, 0).	(0, 0)
end	str or int	How to set cohort_end_date: “observation_period_end_date” (default), “event_end_date”, or a fixed number of days from cohort_start_date.	'observation_period_end_date'
subset_cohort	str	If set, only persons in this cohort table are included.	None
subset_cohort_id	int or list[int]	If set with subset_cohort, only these cohort_definition_id(s) from the subset cohort.	None
overwrite	bool	If True, overwrite existing cohort tables. Default True.	True

Returns

Name	Type	Description
	Cdm	CDM with the new cohort table and cohort_set / cohort_attrition populated.

Raises

Name	Type	Description
	CohortError	If CDM has no database source, name is invalid, or required tables are missing.