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OmopOnPostgres

The goal of OmopOnPostgres is to facilitate working with data in the OMOP CDM format using a PostgreSQL database. The package:

  • Supports multiple database clients: Provides flexible approaches for connecting from R to PostgreSQLs.
  • Simplifies database management: Facilitates the creation, deletion, and management of OMOP CDM schemas and tables directly from
  • Ensures cross-platform compatibility: Enables analytic R packages to reliably use dplyr/dbplyr, supporting cross-platform network studies.
  • Enhances performance: Allows for PostgreSQL-specific optimisations of analytic queries.

Supported drivers

Driver Status (Ubuntu / macOS / Windows)
RPostgres Ubuntu RPostgres macOS RPostgres Windows RPostgres
ADBC Ubuntu ADBC macOS ADBC Windows ADBC
ODBC Ubuntu ODBC macOS ODBC Windows ODBC
DatabaseConnector Ubuntu DatabaseConnector macOS DatabaseConnector Windows DatabaseConnector
DuckDB Ubuntu DuckDB macOS DuckDB Windows DuckDB

Installation

You can install the development version of OmopOnPostgres from GitHub with:

# install.packages("devtools")
devtools::install_github("ohdsi/OmopOnPostgres")

Example 

library(OmopOnPostgres)
library(OmopSketch)
cdm <- mockPostgresCdmReference(client = "RPostgres", 
                                datasetName = "GiBleed")
#> ℹ Loading bundled GiBleed tables from package data.
#> ℹ Adding drug_strength table.
#> ℹ Creating local <cdm_reference> object.
summariseOmopSnapshot(cdm) |> 
  tableOmopSnapshot(type = "flextable")