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CDMConnector

Are you using thetidyversewith an OMOP Common Data Model?

Interact with your CDM in a pipe-friendly way with CDMConnector.

• Quickly connect to your CDM and start exploring.
• Build data analysis pipelines using familiar dplyr verbs.
• Easily extract subsets of CDM data from a database.

Overview

CDMConnector introduces a single R object that represents an OMOP CDMrelational database inspired by thedm,DatabaseConnector,andAndromeda packages.The cdm objects encapsulate references toOMOP CDM tables in aremote RDBMS as well as metadata necessary for interacting with a CDM,allowing for dplyr style data analysis pipelines and interactive dataexploration.

Features

CDMConnector is meant to be the entry point for composable tidyversestyle data analysis operations on an OMOP CDM. Acdm_reference object behaves like a named list oftables.

• Quickly create a list of references to a subset of CDM tables
• Store connection information for later use inside functions
• Use any DBI driver back-end with the OMOP CDM

See Getting started for more details.

Installation

CDMConnector can be installed from CRAN:

install.packages("CDMConnector")

The development version can be installed from GitHub:

# install.packages("devtools")devtools::install_github("darwin-eu/CDMConnector")

Usage

Create a cdm reference from any DBI connection to a databasecontaining OMOP CDM tables. Use the cdm_schema argument to point to aparticular schema in your database that contains your OMOP CDM tablesand the write_schema to specify the schema where results tables can becreated, and use cdm_name to provide a name for the database.

library(CDMConnector)con<- DBI::dbConnect(duckdb::duckdb(dbdir =eunomiaDir()))cdm<-cdmFromCon(con = con,cdmSchema ="main",writeSchema ="main",cdmName ="my_duckdb_database")

Acdm_reference is a named list of table references:

library(dplyr)names(cdm)

##  [1] "person"                "observation_period"    "visit_occurrence"     ##  [4] "visit_detail"          "condition_occurrence"  "drug_exposure"        ##  [7] "procedure_occurrence"  "device_exposure"       "measurement"          ## [10] "observation"           "death"                 "note"                 ## [13] "note_nlp"              "specimen"              "fact_relationship"    ## [16] "location"              "care_site"             "provider"             ## [19] "payer_plan_period"     "cost"                  "drug_era"             ## [22] "dose_era"              "condition_era"         "metadata"             ## [25] "cdm_source"            "concept"               "vocabulary"           ## [28] "domain"                "concept_class"         "concept_relationship" ## [31] "relationship"          "concept_synonym"       "concept_ancestor"     ## [34] "source_to_concept_map" "drug_strength"

Use dplyr verbs with the table references.

cdm$person%>%tally()

## # Source:   SQL [?? x 1]## # Database: DuckDB v1.3.1 [root@Darwin 23.1.0:R 4.3.3//private/var/folders/2j/8z0yfn1j69q8sxjc7vj9yhz40000gp/T/RtmpKZqlCg/file6cc036a4e64a.duckdb]##       n##   <dbl>## 1  2694

Compose operations with the pipe.

cdm$condition_era%>%left_join(cdm$concept,by =c("condition_concept_id"="concept_id"))%>%count(top_conditions = concept_name,sort =TRUE)

## # Source:     SQL [?? x 2]## # Database:   DuckDB v1.3.1 [root@Darwin 23.1.0:R 4.3.3//private/var/folders/2j/8z0yfn1j69q8sxjc7vj9yhz40000gp/T/RtmpKZqlCg/file6cc036a4e64a.duckdb]## # Ordered by: desc(n)##    top_conditions                               n##    <chr>                                    <dbl>##  1 Viral sinusitis                          17268##  2 Acute viral pharyngitis                  10217##  3 Acute bronchitis                          8184##  4 Otitis media                              3561##  5 Osteoarthritis                            2694##  6 Streptococcal sore throat                 2656##  7 Sprain of ankle                           1915##  8 Concussion with no loss of consciousness  1013##  9 Sinusitis                                 1001## 10 Acute bacterial sinusitis                  939## # ℹ more rows

And much more besides. See vignettes for further explanations on howto create database connections, make a cdm reference, and startanalyzing your data.

Getting help

If you encounter a clear bug, please file an issue with a minimalreproducible example onGitHub.

Citation

## To cite package 'CDMConnector' in publications use:## ##   Black A, Gorbachev A, Burn E, Catala Sabate M, Nika I (????).##   _CDMConnector: Connect to an OMOP Common Data Model_. R package##   version 2.1.0, https://github.com/darwin-eu/CDMConnector,##   <https://darwin-eu.github.io/CDMConnector/>.## ## A BibTeX entry for LaTeX users is## ##   @Manual{,##     title = {CDMConnector: Connect to an OMOP Common Data Model},##     author = {Adam Black and Artem Gorbachev and Edward Burn and Marti {Catala Sabate} and Ioanna Nika},##     note = {R package version 2.1.0, https://github.com/darwin-eu/CDMConnector},##     url = {https://darwin-eu.github.io/CDMConnector/},##   }

License: Apache 2.0