pkg_args: setupAthena Arguments

In patelm9/setupAthena: Setup or Update a Postgres Instance of the Athena Vocabularies

setupAthena Arguments

Description

setupAthena Arguments

Arguments

path_to_csvs	Path to folder containing the unpacked vocabularies as csv files, downloaded as a zip from athena.ohdsi.org.
umls_api_key	UMLS API Key for CPT4 reconstitution.
conn	A Postgres connection object from the DatabaseConnector package. The user must either be a superuser or a member of the pg_read_server_files role.
conn_fun	Character string of the expression used to connect to the target database for the setup. The user must either be a superuser or a member of the pg_read_server_files role.This option automatically closes the connection on exit.
verbose	If TRUE, prints back activity in the R console as it is occurring.
render_sql	If TRUE, the SQL statement is printed back in the R console for reference.
target_schema	Schema where the OMOP Vocabulary Tables will be written to.
steps	Options include c("prepare_cpt4", "drop_tables","copy", "indices", "constraints", "log"). Each step corresponds to the function used and may be independently executed.
release_version	Release version as an exact string provided vocabulary download link delivery via email.

patelm9/setupAthena documentation built on June 11, 2024, 4:23 a.m.