Package: CDMConnector 2.5.0

Adam Black

CDMConnector: Connect to an OMOP Common Data Model

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.

Authors:Adam Black [aut, cre], Artem Gorbachev [aut], Edward Burn [aut], Marti Catala Sabate [aut], Ioanna Nika [aut]

CDMConnector_2.5.0.tar.gz
CDMConnector_2.5.0.zip(r-4.7)CDMConnector_2.5.0.zip(r-4.6)CDMConnector_2.5.0.zip(r-4.5)
CDMConnector_2.5.0.tgz(r-4.6-any)CDMConnector_2.5.0.tgz(r-4.5-any)
CDMConnector_2.5.0.tar.gz(r-4.7-any)CDMConnector_2.5.0.tar.gz(r-4.6-any)
CDMConnector_2.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
CDMConnector/json (API)
NEWS

# Install 'CDMConnector' in R:
install.packages('CDMConnector', repos = c('https://darwin-eu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/darwin-eu/cdmconnector/issues

Pkgdown/docs site:https://darwin-eu.github.io

On CRAN:

Conda:

11.74 score 15 stars 10 packages 600 scripts 2.2k downloads 60 exports 44 dependencies

Last updated from:1569ef993e. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK333
source / vignettesOK251
linux-release-x86_64OK336
macos-release-arm64OK301
macos-oldrel-arm64OK228
windows-develOK321
windows-releaseOK370
windows-oldrelOK345
wasm-releaseOK131

Exports:%>%appendPermanentasDateattritionbenchmarkCDMConnectorbindcdmCommentContentscdmConcdmDisconnectcdmFlattencdmFromCohortSetcdmFromConcdmFromTablescdmNamecdmReferencecdmSamplecdmSelectcdmSubsetcdmSubsetCohortcdmVersioncdmWriteSchemacohdSimilarConceptscohortCodelistcohortCountcomputecomputeDataHashByTablecomputeQuerycopyCdmTodateadddatediffdatepartdbmsdbSourcedownloadEunomiaDatadropSourceTabledropTableeunomiaDireunomiaIsAvailableexampleDatasetsgenerateCohortSetgenerateCohortSet2generateConceptCohortSetinSchemainsertCdmToinsertTablelistSourceTableslistTablesnewCohortTablereadCohortSetreadSourceTablerecordCohortAttritionrequireEunomiasettingssnapshotsourceTypesummariseQuantilesummariseQuantile2tblGroupuniqueTableNameversion

Dependencies:askpassbackportsbitbit64blobcheckmateclicliprcpp11crayoncurlDBIdbplyrdplyrgenericsgluehmshttrjsonlitelifecyclemagrittrmimeomopgenericsopensslpillarpkgconfigprettyunitsprogresspurrrR6readrrlangsnakecasestringistringrsystibbletidyrtidyselecttzdbutf8vctrsvroomwithr

CDMConnector and dbplyr

Rendered froma03_dbplyr.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2025-02-10
Started: 2023-03-06

DAG-Based Batch Optimization for Cohort SQL Generation

Rendered froma07_batch-optimization.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2026-03-09
Started: 2026-03-08

DBI connection examples

Rendered froma04_DBI_connection_examples.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2026-02-12
Started: 2023-03-06

Getting Started

Rendered froma01_getting-started.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2025-07-10
Started: 2023-03-06

Incremental DAG Caching for Cohort Generation

Rendered froma08_dag-caching.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2026-03-08
Started: 2026-03-08

Multi-Database Benchmarking: Old vs New Cohort Generation

Rendered froma09_benchmarking.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2026-03-08
Started: 2026-03-08

Using CDM attributes

Rendered froma06_using_cdm_attributes.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2025-02-10
Started: 2023-08-01

Working with cohorts

Rendered froma02_cohorts.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2025-07-10
Started: 2024-01-22

Readme and manuals

Help Manual

Help pageTopics
Run a dplyr query and add the result set to an existingappendPermanent
as.Date dbplyr translation wrapperasDate
Run benchmark of tasks using CDMConnectorbenchmarkCDMConnector
Insert Patient CDM Contents as Aligned Comments in RStudiocdmCommentContents
Get underlying database connectioncdmCon
Disconnect the connection of the cdm objectcdmDisconnect.db_cdm
Flatten a cdm into a single observation tablecdmFlatten
Build a Synthetic CDM from a Cohort SetcdmFromCohortSet
Create a CDM reference object from a database connectioncdmFromCon
Subset a cdm object to a random sample of individualscdmSample
Subset a cdm object to a set of personscdmSubset
Subset a cdm to the individuals in one or more cohortscdmSubsetCohort
Get cdm write schemacdmWriteSchema
Get similar concepts from Columbia Open Health Data (COHD) APIcohdSimilarConcepts
Compute a hash for each CDM tablecomputeDataHashByTable
Execute dplyr query and save result in remote databasecomputeQuery
Copy a cdm object from one database to anothercopyCdmTo
Add days or years to a date in a dplyr querydateadd
Compute the difference between two daysdatediff
Extract the day, month or year of a date in a dplyr pipelinedatepart
Get the database management system (dbms) from a cdm_reference or DBI connectiondbms
Create a source for a cdm in a database.dbSource
Download Eunomia data filesdownloadEunomiaData
Drop table from a database backed cdm objectdropTable.db_cdm
Create a copy of an example OMOP CDM dataseteunomiaDir
Has the Eunomia dataset been cached?eunomiaIsAvailable
List the available example CDM datasetsexampleDatasets
Generate a cohort set on a cdm objectgenerateCohortSet
Generate a cohort set on a CDM object (optimized, no Java dependency)generateCohortSet2
Create a new generated cohort set from a list of concept setsgenerateConceptCohortSet
Helper for working with compound schemainSchema
List tables in a schemalistTables
Read a set of cohort definitions into RreadCohortSet
Require eunomia to be available. The function makes sure that you can later create a eunomia database with 'eunomiaDir()'.requireEunomia
Extract CDM metadatasnapshot
Quantile calculation using dbplyrsummariseQuantile
Quantile calculation using dbplyrsummariseQuantile2
CDM table selection helpertblGroup
Get the CDM versionversion