get_concept function

OMOP Get Concept

This function assists with transforming OMOP concept_ids to interpretable strings by retrieving the requested concepts from the appropriate OMOP concept table.

get_concept(
  table_map,
  db_connection,
  concept_table,
  concept_id,
  concept_name,
  table,
  joinable_id,
  table_concept_id,
  col_name,
  subject_id_field = NULL,
  selected_subject = NULL
)

Arguments

• table_map: A dplyr::tibble containing a mapping between the CDM standard tables and fields to the user connected tables and fields.
• db_connection: A DBI::dbConnect object.
• concept_table: A string, containing the standard CDM concept table name.
• concept_id: A string, containing the standard CDM concept id field.
• concept_name: A string, containing the standard CDM concept name field.
• table: A string, containing the table name that requires OMOP concepts.
• joinable_id: A string, indicating what variable is "joinable" between the concept table and the desired table.
• table_concept_id: A string, containing the the table concept id
• col_name: A string, containing the desired name for the retrieved concept.
• subject_id_field: A string, identifying which table field contains the subject id.
• selected_subject: A numeric, or coercible to numeric containing the desired subject id.

Returns

The desired OMOP concept based on the user data model for all subjects