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Update README with new repo layout
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milanmlft committed Nov 12, 2024
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Expand Up @@ -19,13 +19,22 @@ and subsequently export a selection of concepts of interest.

## Installation

You can install the development version of omopcat from within R like so:
The data catalogue consists of 2 separate R packages:

- [`omopcat`](./app/) defines the [Shiny](https://shiny.posit.co/) app to display the catalogue
- [`omopcat.preprocessing`](./preprocessing/) contains the functionality to summarise an OMOP data source to use as input for the app

The source for these is contained in the `app/` and `preprocessing/` directories, respectively.

You can install the development version of these packages from within R like so:

```r
install.packages("remotes")
usethis::create_github_token()
credentials::set_github_pat()
remotes::install_github("SAFEHR-data/omopcat")

remotes::install_github("SAFEHR-data/omopcat/app") # omopcat
remotes::install_github("SAFEHR-data/omopcat/preprocessing") # omopcat.preprocessing
```

You will need to copy the PAT from the web page that `usethis::create_github_token`
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