Merge branch 'update-function-flow' of https://github.com/steno-aarhu…

…s/osdc into update-function-flow

.github/workflows/assign-author-to-pr.yaml

@@ -0,0 +1,23 @@
+name: Assign author to their PR
+
+on:
+  pull_request:
+    types:
+      - reopened
+      - opened
+
+permissions:
+  pull-requests: write
+
+jobs:
+  assign-author-to-pr:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Assign PR to author
+        run: |
+          gh pr edit $PR --add-assignee $AUTHOR
+        env:
+          AUTHOR: ${{ github.event.pull_request.user.login }}
+          PR: ${{ github.event.pull_request.html_url }}
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+

.github/workflows/puml-to-svg.yaml

@@ -0,0 +1,23 @@
+name: Generate SVG from PlantUML
+
+on:
+  pull_request:
+    paths:
+      - '**.puml'
+
+jobs:
+  generate-plantuml:
+    runs-on: ubuntu-latest
+    steps:
+    - name: checkout
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 1
+
+    - name: plantuml
+      id: plantuml
+      uses: grassedge/[email protected]
+      with:
+        message: "chore: :bento: (re-)generate `.svg` from `.puml` files"
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

DESCRIPTION

@@ -38,7 +38,7 @@ Suggests:
     tibble,
     data.table,
     arrow,
-    duckdb
+    duckplyr
 VignetteBuilder: 
     knitr
 Config/testthat/edition: 3

R/columns-to-lower.R

@@ -6,8 +6,10 @@
 #' @keywords internal
 #'
 #' @examples
+#' \dontrun{
 #' tibble::tibble(A = 1:3, B = 4:6) |>
 #'   osdc:::column_names_to_lower()
+#' }
 column_names_to_lower <- function(data) {
   data |>
     dplyr::rename_with(tolower)

R/get-variables.R

@@ -5,7 +5,9 @@
 #' @keywords internal
 #'
 #' @examples
-#' osdc:::get_register_abbrev()
+#' \dontrun{
+#' get_register_abbrev()
+#' }
 get_register_abbrev <- function() {
   unique(variable_description$register_abbrev)
 }
@@ -19,7 +21,9 @@ get_register_abbrev <- function() {
 #' @keywords internal
 #'
 #' @examples
-#' osdc:::get_required_variables("bef")
+#' \dontrun{
+#' get_required_variables("bef")
+#' }
 get_required_variables <- function(register) {
   if (!checkmate::test_scalar(register)) {
     cli::cli_abort("You are giving too many registers, please give only one.")

R/joins.R

@@ -7,8 +7,10 @@
 #' @keywords internal
 #'
 #' @examples
+#' \dontrun{
 #' register_data$lpr_adm |>
 #'   join_lpr2(register_data$lpr_diag)
+#' }
 join_lpr2 <- function(lpr_adm, lpr_diag) {
   verify_required_variables(lpr_adm, "lpr_adm")
   verify_required_variables(lpr_diag, "lpr_diag")
@@ -28,8 +30,10 @@ join_lpr2 <- function(lpr_adm, lpr_diag) {
 #' @keywords internal
 #'
 #' @examples
+#' \dontrun{
 #' register_data$kontakter |>
 #'   join_lpr3(register_data$diagnoser)
+#' }
 join_lpr3 <- function(kontakter, diagnoser) {
   verify_required_variables(kontakter, "kontakter")
   verify_required_variables(diagnoser, "diagnoser")

R/verify-variables.R

@@ -14,13 +14,15 @@
 #' @keywords internal
 #'
 #' @examples
+#' \dontrun{
 #' # TODO: Replace with simulated data.
 #' verify_required_variables(register_data$bef, "bef")
 #' verify_required_variables(register_data$lpr_adm, "lpr_adm")
+#' }
 verify_required_variables <- function(data, register, call = rlang::caller_env()) {
   checkmate::assert_choice(register, get_register_abbrev())
   expected_variables <- sort(get_required_variables(register))
-  actual_variables <- sort(colnames(data))
+  actual_variables <- tolower(sort(colnames(data)))
 
   if (!checkmate::test_names(
     x = actual_variables,

README.md

@@ -1,4 +1,4 @@
-# osdc: Open Source Diabetes Classifier for Danish Registers
+# osdc <a href="https://steno-aarhus.github.io/osdc/"><img src="man/figures/logo.png" align="right" height="100"/></a>
 
 <!-- badges: start -->
 
@@ -8,14 +8,16 @@ experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](h
 
 <!-- badges: end -->
 
-The goal of *osdc* is to expose an algorithm for classifying diabetes
-within the Danish registers that can be accessible as an R package. The
-algorithm that has been developed at Steno Diabetes Center Aarhus is
-flexible and convenient to use, and validated in terms of accuracy.
-While there are a few algorithms used throughout Denmark for Danish
-register research, they are usually textual descriptions of how to do
-it, rather than code-based descriptions (e.g. the [Register of Selected
-Chronic
+## Overview
+
+The goal of osdc (**O**pen **S**ource **D**iabetes **C**lassifier) is to
+expose an algorithm for classifying diabetes within the Danish registers
+that can be accessible as an R package. The algorithm that has been
+developed at Steno Diabetes Center Aarhus is flexible and convenient to
+use, and validated in terms of accuracy. While there are a few
+algorithms used throughout Denmark for Danish register research, they
+are usually textual descriptions of how to do it, rather than code-based
+descriptions (e.g. the [Register of Selected Chronic
 Diseases](https://www.esundhed.dk/-/media/Files/Publikationer/Emner/Operationer-og-diagnoser/Udvalgte-kroniske-sygdomme-svaere-psykiske-lidelser/Algoritmer-for-Udvalgte-Kroniske-Sygdomme-og-svre-psykiske-lidelser-RUKS-2022.ashx)).
 
 In this project, we aim to make it easier and more explicit to classify

inst/WORDLIST

@@ -33,3 +33,4 @@ polycystic
 pseudonymised
 reproducibility
 semaglutid
+traceback

justfile

@@ -1,10 +1,10 @@
 @_default:
     just --list --unsorted
 
-# Generate PNG images from all PlantUML files
+# Generate svg images from all PlantUML files
 generate-puml-all:
-  docker run --rm -v $(pwd):/puml -w /puml ghcr.io/plantuml/plantuml:1.2024.3 -tpng "**/*.puml"
+  docker run --rm -v $(pwd):/puml -w /puml ghcr.io/plantuml/plantuml:1.2024.3 -tsvg "**/*.puml"
 
-# Generate PNG image from specific PlantUML file
+# Generate svg image from specific PlantUML file
 generate-puml name:
-  docker run --rm -v  $(pwd):/puml -w /puml ghcr.io/plantuml/plantuml:1.2024.3 -tpng "**/{{name}}.puml"
+  docker run --rm -v  $(pwd):/puml -w /puml ghcr.io/plantuml/plantuml:1.2024.3 -tsvg "**/{{name}}.puml"

tests/testthat/helper-options.R

@@ -1,3 +1,11 @@
-# There is a warning when using Arrow about using pull. It says to set
-# this option.
-options(arrow.pull_as_vector = TRUE)
+options(
+  # There is a warning when using Arrow about using pull. It says to set
+  # this option.
+  arrow.pull_as_vector = TRUE,
+  # DuckDB outputs a lot of messages, this stops that.
+  duckdb.materialize_message = FALSE
+)
+# By default, duckplyr logs messages and outputs them when it runs.
+# Adding these options so the test output looks cleaner.
+Sys.setenv(DUCKPLYR_FALLBACK_COLLECT = 0)
+Sys.setenv(DUCKPLYR_FALLBACK_VERBOSE = FALSE)

tests/testthat/test-columns-to-lower.R

@@ -15,7 +15,9 @@ test_that("columns are correctly converted to lowercase", {
 })
 
 test_that("columns are converted for DuckDB Database", {
-  actual <- arrow::to_duckdb(data) |>
+  skip_on_cran()
+  skip_if_not_installed("duckplyr")
+  actual <- duckplyr::as_duckplyr_tibble(data) |>
     column_names_to_lower() |>
     # DuckDB needs to use `colnames()`
     colnames()
@@ -24,6 +26,8 @@ test_that("columns are converted for DuckDB Database", {
 })
 
 test_that("columns are converted for Arrow Tables (from Parquet)", {
+  skip_on_cran()
+  skip_if_not_installed("arrow")
   actual <- arrow::as_arrow_table(data) |>
     column_names_to_lower() |>
     names()
@@ -40,6 +44,8 @@ test_that("columns are converted for data.frame", {
 })
 
 test_that("columns are converted for data.table", {
+  skip_on_cran()
+  skip_if_not_installed("data.table")
   actual <- data.table::as.data.table(data) |>
     column_names_to_lower() |>
     names()

tests/testthat/test-include-hba1c.R

@@ -58,7 +58,9 @@ test_that("casing of input variables doesn't matter", {
 })
 
 test_that("verification works for DuckDB Database", {
-  actual <- arrow::to_duckdb(lab_forsker) |>
+  skip_on_cran()
+  skip_if_not_installed("duckplyr")
+  actual <- duckplyr::as_duckplyr_tibble(lab_forsker) |>
     include_hba1c()
 
   actual_rows <- actual |>
@@ -70,6 +72,8 @@ test_that("verification works for DuckDB Database", {
 })
 
 test_that("verification works for Arrow Tables (from Parquet)", {
+  skip_on_cran()
+  skip_if_not_installed("arrow")
   actual <- arrow::as_arrow_table(lab_forsker) |>
     include_hba1c() |>
     # TODO: Arrow doesn't like the `row_number()` function, find a fix?
@@ -97,6 +101,8 @@ test_that("verification works for data.frame", {
 })
 
 test_that("verification works for data.table", {
+  skip_on_cran()
+  skip_if_not_installed("data.table")
   actual <- data.table::as.data.table(lab_forsker) |>
     include_hba1c()