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Create a new generated cohort set from a list of concept sets

Source: R/generateConceptCohortSet.R
generateConceptCohortSet.Rd

Generate a new cohort set from one or more concept sets. Each concept set will result in one cohort and represent the time during which the concept was observed for each subject/person. Concept sets can be passed to this function as:

  • A named list of numeric vectors, one vector per concept set

  • A named list of Capr concept sets

Clinical observation records will be looked up in the respective domain tables using the vocabulary in the CDM. If a required domain table does not exist in the cdm object a warning will be given. Concepts that are not in the vocabulary or in the data will be silently ignored. If end dates are missing or do not exist, as in the case of the procedure and observation domains, the the start date will be used as the end date.

Usage

generateConceptCohortSet(
  cdm,
  conceptSet = NULL,
  name,
  limit = "first",
  requiredObservation = c(0, 0),
  end = "observation_period_end_date",
  subsetCohort = NULL,
  subsetCohortId = NULL,
  overwrite = TRUE
)

generate_concept_cohort_set(
  cdm,
  concept_set = NULL,
  name = "cohort",
  limit = "first",
  required_observation = c(0, 0),
  end = "observation_period_end_date",
  subset_cohort = NULL,
  subset_cohort_id = NULL,
  overwrite = TRUE
)

Arguments

cdm

A cdm reference object created by CDMConnector::cdmFromCon or CDMConnector::cdm_from_con

conceptSet, concept_set

A named list of numeric vectors or a Concept Set Expression created omopgenerics::newConceptSetExpression

name

The name of the new generated cohort table as a character string

limit

Include "first" (default) or "all" occurrences of events in the cohort

  • "first" will include only the first occurrence of any event in the concept set in the cohort.

  • "all" will include all occurrences of the events defined by the concept set in the cohort.

requiredObservation, required_observation

A numeric vector of length 2 that specifies the number of days of required observation time prior to index and post index for an event to be included in the cohort.

end

How should the cohort_end_date be defined?

  • "observation_period_end_date" (default): The earliest observation_period_end_date after the event start date

  • numeric scalar: A fixed number of days from the event start date

  • "event_end_date": The event end date. If the event end date is not populated then the event start date will be used

subsetCohort, subset_cohort

A cohort table containing the individuals for which to generate cohorts for. Only individuals in the cohort table will appear in the created generated cohort set.

subsetCohortId, subset_cohort_id

A set of cohort IDs from the cohort table for which to include. If none are provided, all cohorts in the cohort table will be included.

overwrite

Should the cohort table be overwritten if it already exists? TRUE (default) or FALSE.

Value

A cdm reference object with the new generated cohort set table added