Create minimal R package

.Rbuildignore

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+^renv$
+^renv\.lock$
+^.*\.Rproj$
+^\.Rproj\.user$
+^.lintr$
+^.github$

.Rprofile

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+source("renv/activate.R")

.github/workflows/R-CMD-check.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+ R-CMD-check:
+ runs-on: ubuntu-latest
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ R_KEEP_PKG_SOURCE: yes
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-renv@v2
+
+ - name: Install rcmdcheck
+ run: install.packages("rcmdcheck")
+ shell: Rscript {0}
+
+ - uses: r-lib/actions/check-r-package@v2
+ with:
+ upload-snapshots: true
+ build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/lint.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+
+name: lint.yaml
+
+permissions: read-all
+
+jobs:
+ lint:
+ runs-on: ubuntu-latest
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-renv@v2
+
+ - name: Install lintr
+ run: install.packages("lintr")
+ shell: Rscript {0}
+
+ - name: Lint
+ run: |
+ pkgload::load_all()
+ lintr::lint_package()
+ shell: Rscript {0}
+ env:
+ LINTR_ERROR_ON_LINT: true

.github/workflows/pr-commands.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+ issue_comment:
+ types: [created]
+
+name: pr-commands.yaml
+
+permissions: read-all
+
+jobs:
+ document:
+ if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+ name: document
+ runs-on: ubuntu-latest
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ permissions:
+ contents: write
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/pr-fetch@v2
+ with:
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-renv@v2
+
+ - name: Install roxygen2
+ run: install.packages("roxygen2")
+ shell: Rscript {0}
+
+ - name: Document
+ run: roxygen2::roxygenise()
+ shell: Rscript {0}
+
+ - name: commit
+ run: |
+ git config --local user.name "$GITHUB_ACTOR"
+ git config --local user.email "[email protected]"
+ git add man/\* NAMESPACE
+ git commit -m 'Document'
+
+ - uses: r-lib/actions/pr-push@v2
+ with:
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+ style:
+ if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+ name: style
+ runs-on: ubuntu-latest
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ permissions:
+ contents: write
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/pr-fetch@v2
+ with:
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+ - uses: r-lib/actions/setup-r@v2
+
+ - name: Install dependencies
+ run: install.packages("styler")
+ shell: Rscript {0}
+
+ - name: Style
+ run: styler::style_pkg()
+ shell: Rscript {0}
+
+ - name: commit
+ run: |
+ git config --local user.name "$GITHUB_ACTOR"
+ git config --local user.email "[email protected]"
+ git add \*.R
+ git commit -m 'Style'
+
+ - uses: r-lib/actions/pr-push@v2
+ with:
+ repo-token: ${{ secrets.GITHUB_TOKEN }}

.lintr

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+linters: linters_with_defaults(
+ line_length_linter(120),
+ object_name_linter(styles = c("snake_case", "symbols", "camelCase"))
+ )
+encoding: "UTF-8"

DESCRIPTION

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+Package: omopbundles
+Type: Package
+Title: Bundles of OMOP Concepts for Ease of Data Selection
+Version: 0.1.0
+Authors@R: person('Stef', 'Piatek', email = '[email protected]', role = c('cre', 'aut'))
+Description: Bundles of OMOP Concepts for Ease of Data Selection.
+License: Apache License (>= 2)
+Encoding: UTF-8
+LazyData: true
+Imports:
+ dplyr (>= 1.0),
+ purrr (>= 1.0),
+ readr (>= 2.0)
+Suggests:
+ devtools,
+ usethis,
+ testthat (>= 3.0.0),
+ lintr,
+ pak,
+ pkgload
+Config/testthat/edition: 3
+RoxygenNote: 7.3.2

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(available_bundles)
+export(concept_by_bundle)
+importFrom(dplyr,mutate)
+importFrom(dplyr,tibble)
+importFrom(purrr,map_dfr)
+importFrom(readr,read_csv)

R/bundles.R

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+#' @importFrom dplyr tibble mutate
+#' @importFrom purrr map_dfr
+#' @importFrom readr read_csv
+
+#' @title Get available bundles for a version
+#'
+#' @description If a bundle has multiple names, then the id will be duplicated across rows
+#'
+#' @param version Requested version, if not defined, the latest will be used
+#' @return dataframe that contains a "concept_name", "version" and a "domain" column for each available concept
+#' @export
+#' @examples
+#' available_bundles()
+#' available_bundles("0.1")
+available_bundles <- function(version = "latest") {
+ raw_dir <- .get_raw_dir(version = version)
+ directories <- list.dirs(raw_dir, full.names = TRUE)
+ domain_directories <- directories[directories != raw_dir]
+
+ purrr::map_dfr(domain_directories, .build_concepts_from_directory) |>
+ mutate(version = version)
+}
+
+.get_raw_dir <- function(version, ...) {
+ if (version != "latest") warning("Versioning not yet implemented, using version = 'latest'")
+
+ system.file("data-raw", ..., package = "omopbundles", mustWork = TRUE)
+}
+
+.build_concepts_from_directory <- function(directory) {
+ concept_files <- list.files(directory)
+ concept_name <- NULL
+
+ dplyr::tibble(
+ id = concept_files,
+ concept_name = concept_files,
+ domain = basename(directory)
+ ) |>
+ dplyr::mutate(concept_name = sub("\\.csv$", "", concept_name)) |>
+ dplyr::mutate(concept_name = gsub("_", " ", concept_name))
+}
+
+
+#' @title Get concepts for a a single bundle row
+#'
+#' @description Retrieves concept data for a specific bundle.
+#'
+#' @param domain The domain of the bundle.
+#' @param id The ID of the bundle.
+#' @param version The version of the bundle. Default is "latest".
+#' @return A data frame with the concept data.
+#' @export
+#' @examples
+#' # Usage with available_bundles, from a single row
+#' smoking_info <- available_bundles() |> dplyr::filter(concept_name == "smoking")
+#' concept_by_bundle(domain = smoking_info$domain, id = smoking_info$id, version = smoking_info$version)
+#' # Using if you know the details directly
+#' concept_by_bundle(domain = "observation", id = "smoking.csv")
+concept_by_bundle <- function(domain, id, version = "latest") {
+ .get_raw_dir(version = version, domain, id) |>
+ readr::read_csv(show_col_types = FALSE) |>
+ dplyr::mutate(domain = domain)
+}

README.md

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-# omop-bundles
-R package to provide access to OMOP bundles
+# Omop Bundles
+
+<!-- badges: start -->
+[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![R-CMD-check](https://github.com/SAFEHR-data/omop-bundles/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/SAFEHR-data/omop-bundles/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->
+
+Catalogue of omop concepts grouped into useful bundles to help researchers select concepts. 
+
+## Overview
+
+1. [Installation](#installation)
+2. [Development](#development)
+ - [Set up](#set-up)
+ - [Updating the `renv` lockfile](#updating-the-renv-lockfile)
+ - [Design](#design)
+ - [Coding style](#coding-style)
+3. [Deployment](./deploy/README.md)
+
+## Installation
+
+You can install the development version of data-catalogue from within R:
+
+```r
+# install.packages("pak")
+pak::pak("SAFEHR-data/data-catalogue")
+```
+
+## Development
+
+### Set up
+
+Make sure you have a [recent version of R](https://cloud.r-project.org/) (>= 4.4.0) installed.
+Though not required, [RStudio](https://www.rstudio.com/products/rstudio/download/) 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](https://docs.posit.co/ide/user/ide/guide/tools/version-control.html#creating-a-new-project-based-on-a-remote-git-or-subversion-repository)
+
+2. Install [`{renv}`](https://rstudio.github.io/renv/index.html) and restore the project library by running the following from an R console in the project directory:
+
+ ```r
+ 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
+
+```r
+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
+
+```r
+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](https://style.tidyverse.org/).
+The [`{styler}`](https://styler.r-lib.org/index.html) package can be used to automatically format R code to this style,
+by regularly running
+
+```r
+styler::style_pkg()
+```
+
+within the project directory.
+It's also recommended to install [`{lintr}`](https://github.com/r-lib/lintr) and regularly run
+
+```r
+lintr::lint_package()
+```
+
+(or have it [run automatically in your IDE](https://lintr.r-lib.org/articles/editors.html)).

inst/data-raw/measurement/HBA1c.csv

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+concept_id,allowed,per_person,min,max
+3005673,T,1,0,
+40762352,T,1,0,
+

inst/data-raw/measurement/LDH.csv

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+concept_id,allowed,per_person,min,max
+3022250,T,1,0,
+

inst/data-raw/measurement/antibodies_to_hiv.csv

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+concept_id,allowed,per_person,min,max
+40760007,T,1,0,
+