CDMConnector1.7.0 package

Connect to an OMOP Common Data Model

appendPermanent

Run a dplyr query and add the result set to an existing

asDate

as.Date dbplyr translation wrapper

assert_write_schema

Assert that cdm has a writable schema

assertTables

Assert that tables exist in a cdm object

benchmarkCDMConnector

Run benchmark of tasks using CDMConnector

cdm_from_tables

Create a cdm object from local tables

cdm_name

Get the CDM name

cdmCon

Get underlying database connection

CDMConnector-package

CDMConnector: Connect to an OMOP Common Data Model

cdmDisconnect

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

cdmFromEnvironment

Create a CDM object from a pre-defined set of environment variables

cdmFromFiles

Create a CDM reference from a folder containing parquet, csv, or feath...

cdmSample

Subset a cdm object to a random sample of individuals

cdmSelectTbl

Select a subset of tables in a cdm reference object

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

cohort_count

Get cohort counts from a generated_cohort_set object.

cohortAttrition

Get attrition table from a cohort_table object

cohortErafy

Collapse cohort records within a certain number of days

cohortSet

Get cohort settings from a cohort_table object

cohortUnion

Union all cohorts in a cohort set with cohorts in a second cohort set

computeQuery

Execute dplyr query and save result in remote database

copyCdmTo

Copy a cdm object from one database to another

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

dbms

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

dbSource

Create a source for a cdm in a 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

generateCohortSet

Generate a cohort set on a cdm object

generateConceptCohortSet

Create a new generated cohort set from a list of concept sets

inSchema

Helper for working with compound schemas

intersectCohorts

Intersect all cohorts in a single cohort table

listTables

List tables in a schema

new_generated_cohort_set

Constructor for cohort_table objects

pipe

Pipe operator

readCohortSet

Read a set of cohort definitions into R

record_cohort_attrition

Add attrition reason to a cohort_table object

reexports

Objects exported from other packages

requireEunomia

Require eunomia to be available. The function makes sure that you can ...

snapshot

Extract CDM metadata

stow

Collect a list of lazy queries and save the results as files

summariseQuantile

Quantile calculation using dbplyr

tblGroup

CDM table selection helper

unionCohorts

Union all cohorts in a single cohort table

unique_table_name

Create a unique table name for temp tables

validateCdm

Validation report for a CDM

version

Get the CDM version

Provides tools for working with observational health data in the Observational Medical Outcomes Partnership (OMOP) Common Data Model format with a pipe friendly syntax. Common data model database table references are stored in a single compound object along with metadata.

  • Maintainer: Adam Black
  • License: Apache License (>= 2)
  • Last published: 2024-12-19