Package index • CDMConnector

CDM Object

Create or transform a CDM reference object. These accept and return cdm objects.

cdmCon(): Get underlying database connection

cdmDisconnect(<db_cdm>): Disconnect the connection of the cdm object

cdmFlatten(): Flatten a cdm into a single observation table

cdmFromCon(): Create a CDM reference object from a database connection

cdmSample(): Subset a cdm object to a random sample of individuals

cdmSubset(): Subset a cdm object to a set of persons

cdmSubsetCohort(): Subset a cdm to the individuals in one or more cohorts

cdmWriteSchema(): Get cdm write schema

computeDataHashByTable(): Compute a hash for each CDM table

copyCdmTo(): Copy a cdm object from one database to another

dbSource(): Create a source for a cdm in a database.

dropTable(<db_cdm>): Drop table from a database backed cdm object

snapshot(): Extract CDM metadata

tblGroup(): CDM table selection helper

version(): Get the CDM version

Cohort Creation and Transformation

A cohort is a set of person-days representing the time during which people in a CDM exhibited some observable characteristics. Cohorts are often the foundation of downstream analyses.

generateCohortSet() experimental: Generate a cohort set on a cdm object

generateConceptCohortSet(): Create a new generated cohort set from a list of concept sets

readCohortSet(): Read a set of cohort definitions into R

summariseQuantile(): Quantile calculation using dbplyr

summariseQuantile2(): Quantile calculation using dbplyr

dbplyr workarounds

Functions that can be used in cross database dplyr pipelines

appendPermanent(): Run a dplyr query and add the result set to an existing

asDate(): as.Date dbplyr translation wrapper

computeQuery(): Execute dplyr query and save result in remote database

dateadd(): Add days or years to a date in a dplyr query

datediff(): Compute the difference between two days

datepart(): Extract the day, month or year of a date in a dplyr pipeline

inSchema(): Helper for working with compound schemas

DBI connection

Functions that accept DBI connections and are useful in cross database DBI code

dbms(): Get the database management system (dbms) from a cdm_reference or DBI connection

listTables(): List tables in a schema

Eunomia example CDM

Easily create and use example CDMs in a duckdb database

downloadEunomiaData(): Download Eunomia data files

eunomiaDir(): Create a copy of an example OMOP CDM dataset

eunomiaIsAvailable(): Has the Eunomia dataset been cached?

exampleDatasets(): List the available example CDM datasets

requireEunomia(): Require eunomia to be available. The function makes sure that you can later create a eunomia database with eunomiaDir().

Benchmarking

Run benchmarking of simple queries against your CDM reference

benchmarkCDMConnector(): Run benchmark of tasks using CDMConnector