Package index • OmopOnPostgres

Create a cdm_reference

cdmFromPostgres(): Create a <cdm_reference> object from a postgres connection

Copy a cdm_reference to a postgres source

copyCdmToPostgres(): Copy a cdm (independently of its source) to a

Create empty OMOP CDM tables

createOmopTablesOnPostgres(): Title

Create and read logging files

postgresLog(): Start a postgres log
readPostgresLog(): Create a tibble from the log files in the logPath folder

Job management

Cancel and manage jobs.

getJobs(): Get ongoing Postgres jobs.
cancelJob(): Cancel a Postgres job.
getUserTables(): Get tables created by a user in a schema.

Index mangement

Create and check existing indexes.

reexports expectedIndexes existingIndexes statusIndexes createIndexes createTableIndex listSourceTables insertTable dropSourceTable insertCdmTo readSourceTable cdmDisconnect cdmTableFromSource compute: Objects exported from other packages

Create a postgres source object

postgresSource(): Create a postgres source object

CDM object managment

Reexported functions from other packages for the cdm_reference object management.

reexports expectedIndexes existingIndexes statusIndexes createIndexes createTableIndex listSourceTables insertTable dropSourceTable insertCdmTo readSourceTable cdmDisconnect cdmTableFromSource compute: Objects exported from other packages

Create a local postgres

Create a local postgres connection using environmental variables.

localPostgres(): This function creates a connection to the local postgres instance
mockPostgresCdmReference(): Mock Postgres CDM reference

Benchmark postgres

Assess time to collect from and insert data into a postgres cdm reference

benchmarkOmopOnPostgres(): Benchmark OMOP on Postgres

DuckDb utilities

Utilities to support working with DuckDb and Postgres

attachPgDb(): Attach a postres database to a duckdb database
duckdbHasPgDbAttached(): Check if a PostgreSQL database is attached to DuckDB
duckdbUsePgDb(): Ensure duckdb is using Postgres as default catalog
duckdbUseDuckDb(): Ensure duckdb is using the native DuckDB catalog
duckdbIsUsingPgDb(): Check if duckdb is using Postgres as default catalog