Package: CDMConnector 2.0.0

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]

CDMConnector_2.0.0.tar.gz
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CDMConnector.pdf |CDMConnector.html✨
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 site:https://darwin-eu.github.io

On CRAN:

Conda:

11.39 score 12 stars 12 packages 502 scripts 1.7k downloads 53 exports 39 dependencies

Last updated 10 days agofrom:d49e06465d. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 26 2025
R-4.5-winOKFeb 26 2025
R-4.5-macOKFeb 26 2025
R-4.5-linuxOKFeb 26 2025
R-4.4-winOKFeb 26 2025
R-4.4-macOKFeb 26 2025
R-4.3-winOKFeb 26 2025
R-4.3-macOKFeb 26 2025

Exports:%>%appendPermanentasDateattritionbenchmarkCDMConnectorbindcdmConcdmDisconnectcdmFlattencdmFromConcdmFromTablescdmNamecdmSamplecdmSelectcdmSubsetcdmSubsetCohortcdmVersioncdmWriteSchemacohortCodelistcohortCountcomputecomputeQuerycopyCdmTodateadddatediffdatepartdbmsdbSourcedownloadEunomiaDatadropSourceTabledropTabledropTable.db_cdmeunomiaDireunomiaIsAvailableexampleDatasetsgenerateCohortSetgenerateConceptCohortSetinSchemainsertCdmToinsertTablelistSourceTableslistTablesnewCohortTablereadCohortSetreadSourceTablerecordCohortAttritionrequireEunomiasettingssnapshotsummariseQuantiletblGroupuniqueTableNameversion

Dependencies:backportsbitbit64blobcheckmateclicliprcpp11crayonDBIdbplyrdplyrfansigenericsgluehmsjsonlitelifecyclemagrittromopgenericspillarpkgconfigprettyunitsprogresspurrrR6readrrlangsnakecasestringistringrtibbletidyrtidyselecttzdbutf8vctrsvroomwithr

CDMConnector and dbplyr

Rendered froma03_dbplyr.Rmdusingknitr::rmarkdownon Feb 26 2025.

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

DBI connection examples

Rendered froma04_DBI_connection_examples.Rmdusingknitr::rmarkdownon Feb 26 2025.

Last update: 2024-12-05
Started: 2023-03-06

Getting Started

Rendered froma01_getting-started.Rmdusingknitr::rmarkdownon Feb 26 2025.

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

Using CDM attributes

Rendered froma06_using_cdm_attributes.Rmdusingknitr::rmarkdownon Feb 26 2025.

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

Working with cohorts

Rendered froma02_cohorts.Rmdusingknitr::rmarkdownon Feb 26 2025.

Last update: 2025-02-10
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
Get underlying database connectioncdmCon
Disconnect the connection of the cdm objectcdmDisconnect.db_cdm
Flatten a cdm into a single observation tablecdmFlatten
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
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
Create a new generated cohort set from a list of concept setsgenerateConceptCohortSet
Helper for working with compound schemasinSchema
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
CDM table selection helpertblGroup
Get the CDM versionversion