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A pipe friendly way to interact with an OMOP Common Data Model
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darwin-eu/CDMConnector
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Are you using thetidyverse with an OMOPCommon 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.
CDMConnector introduces a single R object that represents an OMOP CDMrelational database inspired by thedm,DatabaseConnector, andAndromeda packages. The cdmobjects encapsulate references toOMOP CDMtables in a remote RDBMS aswell as metadata necessary for interacting with a CDM, allowing fordplyr style data analysis pipelines and interactive data exploration.
CDMConnector is meant to be the entry point for composable tidyversestyle data analysis operations on an OMOP CDM. Acdm_reference objectbehaves like a named list of tables.
- 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.
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")
Create a cdm reference from any DBI connection to a database containingOMOP CDM tables. Use the cdm_schema argument to point to a particularschema in your database that contains your OMOP CDM tables and thewrite_schema to specify the schema where results tables can be created,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$person %>% tally()
## # Source: SQL [?? x 1]## # Database: DuckDB v1.3.1 [root@Darwin 23.1.0:R 4.3.3//private/var/folders/2j/8z0yfn1j69q8sxjc7vj9yhz40000gp/T/RtmpKZqlCg/file6cc036a4e64a.duckdb]## n## <dbl>## 1 2694Compose operations with the pipe.
cdm$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 rowsAnd much more besides. See vignettes for further explanations on how tocreate database connections, make a cdm reference, and start analyzingyour data.
If you encounter a clear bug, please file an issue with a minimalreproducible example onGitHub.
## 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
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