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https://github.com/ablack3/cdmconnector
https://github.com/ablack3/cdmconnector
Last synced: 12 days ago
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- Host: GitHub
- URL: https://github.com/ablack3/cdmconnector
- Owner: ablack3
- License: apache-2.0
- Created: 2024-05-14T10:03:03.000Z (7 months ago)
- Default Branch: main
- Last Pushed: 2024-05-14T15:08:51.000Z (7 months ago)
- Last Synced: 2024-05-15T16:04:29.115Z (7 months ago)
- Language: HTML
- Size: 27.3 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
---
output: github_document
---
# [CDMConnector](https://darwin-eu.github.io/CDMConnector/)
[](https://CRAN.R-project.org/package=CDMConnector)
[](https://app.codecov.io/gh/darwin-eu/CDMConnector?branch=main)
[](https://github.com/darwin-eu/CDMConnector/actions?query=workflow%3AR-CMD-check)
[](https://github.com/darwin-eu/CDMConnector/actions?query=workflow%3Aduckdb-test)
[](https://github.com/darwin-eu/CDMConnector/actions?query=workflow%3Apostgres-test)
[](https://github.com/darwin-eu/CDMConnector/actions?query=workflow%3Asqlserver-odbc-test)
[](https://github.com/darwin-eu/CDMConnector/actions?query=workflow%3Aredshift-test)
[](https://github.com/darwin-eu/CDMConnector/actions?query=workflow%3Asnowflake-odbc-test)
> Are you using the [tidyverse](https://www.tidyverse.org/) with 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 CDM relational database inspired by the [dm](https://dm.cynkra.com/), [DatabaseConnector](http://ohdsi.github.io/DatabaseConnector/), and [Andromeda](https://ohdsi.github.io/Andromeda/) packages. The cdm objects encapsulate references to [OMOP CDM tables](https://ohdsi.github.io/CommonDataModel/) in a remote RDBMS as well as metadata necessary for interacting with a CDM, allowing for dplyr style data analysis pipelines and interactive data exploration.
[](https://ohdsi.github.io/CommonDataModel/)
## Features
CDMConnector is meant to be the entry point for composable tidyverse style data analysis operations on an OMOP CDM.
A `cdm_reference` object behaves 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.
## Installation
CDMConnector can be installed from CRAN:
```r
install.packages("CDMConnector")
```
The development version can be installed from GitHub:
```r
# install.packages("devtools")
devtools::install_github("darwin-eu/CDMConnector")
```
## Usage
Create a cdm reference from any DBI connection to a database containing OMOP CDM tables. Use the cdm_schema argument to point to a particular schema in your database that contains your OMOP CDM tables and the write_schema to specify the schema where results tables can be created, and use cdm_name to provide a name for the database.
```{r}
library(CDMConnector)
con <- DBI::dbConnect(duckdb::duckdb(dbdir = eunomia_dir()))
cdm <- cdm_from_con(con = con,
cdm_schema = "main",
write_schema = "main",
cdm_name = "my_duckdb_database")
```
A `cdm_reference` is a named list of table references:
```{r, warning=FALSE, message=FALSE}
library(dplyr)
names(cdm)
```
Use dplyr verbs with the table references.
```{r}
cdm$person %>%
tally()
```
Compose operations with the pipe.
```{r}
cdm$condition_era %>%
left_join(cdm$concept, by = c("condition_concept_id" = "concept_id")) %>%
count(top_conditions = concept_name, sort = TRUE)
```
And much more besides. See vignettes for further explanations on how to create database connections, make a cdm reference, and start analysing your data.
```{r, include=FALSE}
cdmDisconnect(cdm)
```
## Getting help
If you encounter a clear bug, please file an issue with a minimal [reproducible example](https://reprex.tidyverse.org/) on [GitHub](https://github.com/darwin-eu/CDMConnector/issues).
---
License: Apache 2.0