We’ve written this book for anyone interested in a working with databases using a tidyverse style approach. That is, human centered, consistent, composable, and inclusive (see https://design.tidyverse.org/unifying.html for more details on these principles).
New to R? We recommend you compliment the book with R for data science
New to databases? We recommend you take a look at some web tutorials on SQL, such as SQLBolt or SQLZoo
New to the OMOP CDM? We’d recommend you pare this book with The Book of OHDSI
The book is divided into two parts. The first half of the book is focused on the general principles for working with databases from R. In these chapters you will see how you can use familiar tidyverse-style code to build up analytic pipelines that start with data held in a database and end with your analytic results. The second half of the book is focused on working with data in the OMOP Common Data Model (CDM) format, a widely used data format for health care data. In these chapters you will see how to work with this data format using the general principles from the first half of the book along with a set of R packages that have been built for the OMOP CDM.
TO ADD
The source code for the book can be found at this Github repository
This book is rendered using the following version of packages:
Finding R package dependencies ... Done!| Package | Version | Link |
|---|---|---|
| CDMConnector | 2.1.1 | 🔗 |
| CodelistGenerator | 3.5.0 | 🔗 |
| CohortCharacteristics | 1.0.0 | 🔗 |
| CohortConstructor | 0.5.0 | 🔗 |
| DBI | 1.2.3 | 🔗 |
| Lahman | 13.0-0 | 🔗 |
| PatientProfiles | 1.4.2 | 🔗 |
| bit64 | 4.6.0-1 | 🔗 |
| cli | 3.6.5 | 🔗 |
| clock | 0.7.3 | 🔗 |
| dbplyr | 2.5.1 | 🔗 |
| dm | 1.0.12 | 🔗 |
| dplyr | 1.1.4 | 🔗 |
| duckdb | 1.3.3 | 🔗 |
| ggplot2 | 3.5.2 | 🔗 |
| here | 1.0.1 | 🔗 |
| omock | 0.5.0 | 🔗 |
| omopgenerics | 1.3.0 | 🔗 |
| palmerpenguins | 0.1.1 | 🔗 |
| purrr | 1.1.0 | 🔗 |
| sloop | 1.0.1 | 🔗 |
| stringr | 1.5.2 | 🔗 |
| tidyr | 1.3.1 | 🔗 |
Note we only included the packages called explicitly in the book.