Omop Bundles

Catalogue of omop concepts grouped into useful bundles to help researchers select concepts.

Overview

1. Installation
2. Development
   • Set up
   • Updating the renv lockfile
   • Design
   • Coding style
3. Deployment

Installation

You can install the development version of data-catalogue from within R:

# install.packages("pak")
pak::pak("SAFEHR-data/omop-bundles")

Development

Set up

Make sure you have a recent version of R (>= 4.4.0) installed. Though not required, RStudio is recommended as an IDE, as it has good support for R package development and Shiny.

1. Clone this repository

   • Either with git clone [email protected]:SAFEHR-data/omop-bundles.git
   • Or by creating a new project in RStudio from version control

2. Install {renv} and restore the project library by running the following from an R console in the project directory:

   install.packages("renv")
   renv::restore()

Updating the renv lockfile

Make sure to regularly run renv::status(dev = TRUE) to check if your local library and the lockfile are up to date.

When adding a new dependency, install it in the renv library with

renv::install("package_name")

and then use it in your code as usual. renv will pick up the new package if it's installed and used in the project.

To update the lockfile, run

renv::snapshot(dev = TRUE)

The dev = TRUE argument ensures that development dependencies (e.g. those recorded under Suggests in the DESCRIPTION file) are also included in the lockfile.

Coding style

We are following the tidyverse style guide. The {styler} package can be used to automatically format R code to this style, by regularly running

styler::style_pkg()

within the project directory. It's also recommended to install {lintr} and regularly run

lintr::lint_package()

(or have it run automatically in your IDE).