fetch_omop_relationships: Fetch OMOP Relationships

In meerapatelmd/chariotViz: Visualize the OMOP Vocabularies

Description

Fetch concept class relationships in a Postgres instance of the OMOP vocabularies.

Usage

fetch_omop_relationships(
  ...,
  conn,
  conn_fun = "pg13::local_connect(verbose=FALSE)",
  schema = "omop_vocabulary",
  verbose = FALSE,
  render_sql = FALSE,
  version_key
)

Arguments

conn	PARAM_DESCRIPTION
conn_fun	PARAM_DESCRIPTION, Default: 'pg13::local_connect(verbose=FALSE)'
schema	PARAM_DESCRIPTION, Default: 'omop_vocabulary'
verbose	PARAM_DESCRIPTION, Default: FALSE
render_sql	PARAM_DESCRIPTION, Default: FALSE
version_key	A list object that serves as the hash for caching. Set to NULL to cache under a generic hash.
type_from	PARAM_DESCRIPTION, Default: concept_class_id

Details

The OMOP vocabularies are transformed into nodes and edges by first normalizing OMOP concepts to their associated concept classes. The distinct concept_id count is preserved to determine the extent of coverage between concept classes across relationships.

This function queries excludes invalid concepts and concept relationships as well as relationships to self.

Value

OUTPUT_DESCRIPTION

meerapatelmd/chariotViz documentation built on Dec. 21, 2021, 4:53 p.m.