generateConceptCohortSet {CDMConnector}

R Documentation

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

Description

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 = "cohort",
  limit = "first",
  requiredObservation = c(0, 0),
  end = "observation_period_end_date",
  overwrite = FALSE
)

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

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 Capr concept sets
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
overwrite	Should the cohort table be overwritten if it already exists? TRUE or FALSE (default)

Value

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

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