Merge branch 'main' into feat/list-needed-vars

Author: lwjohnst86

DESCRIPTION

@@ -1,6 +1,6 @@
 Type: Package
 Package: osdc
-Title: Open Source Diabetes Classifier for Danish Registers.
+Title: Open Source Diabetes Classifier (OSCD) for Danish Registers
 Version: 0.0.1.9000
 Authors@R: c(
     person(
@@ -51,8 +51,6 @@ Imports:
     purrr,
     rlang
 Suggests:
-    furrr,
-    DiagrammeR,
     knitr,
     rmarkdown,
     testthat (>= 3.0.0),

R/verify-variables.R

@@ -20,12 +20,12 @@
 #' verify_required_variables(example_bef_data, "bef")
 verify_required_variables <- function(data, register) {
   checkmate::assert_choice(register, get_register_abbrev())
-
+  
+  # TODO: Consider using/looking into rlang::try_fetch() to provide contextual error messages.
   expected_variables <- get_required_variables(register)
 
-  actual_variables <- names(data)
-
-  # TODO: Consider using/looking into rlang::try_fetch() to provide contextual error messages.
+  actual_variables <- colnames(data)
+  
   checkmate::check_names(
     x = actual_variables,
     must.include = expected_variables

README.md

@@ -3,21 +3,21 @@
 <!-- badges: start -->
 
 [![R-CMD-check](https://github.com/steno-aarhus/osdc/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/steno-aarhus/osdc/actions/workflows/R-CMD-check.yaml)
-
+[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 <!-- 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 has been developed at Steno Diabetes Center Aarhus that is
+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 in
-classifying type 1 and type 2 diabetes within a Danish register context.
+In this project, we aim to make it easier and more explicit to
+classify type 1 and type 2 diabetes within a Danish register context.
 The original implementation of the algorithm is validated in a
 peer-reviewed publication [here](https://doi.org/10.2147/clep.s407019),
 but we expect to make tweaks to the algorithm over time. Any changes

man/hello.Rd

@@ -1,8 +1,8 @@
 library(tibble)
 
-test_that("the correct abbreviation for the register is used", {
-  bef_complete <- tibble(pnr = 1, koen = 1, foed_dato = 1)
+bef_complete <- tibble::tibble(pnr = 1, koen = 1, foed_dato = 1)
 
+test_that("the correct abbreviation for the register is used", {
   # When incorrect register abbreviation is given
   expect_error(verify_required_variables(bef_complete, "bef1"))
   # When correct abbreviation is given
@@ -11,7 +11,6 @@ test_that("the correct abbreviation for the register is used", {
 
 test_that("the required variables are present in the dataset", {
   # Expected
-  bef_complete <- tibble(pnr = 1, koen = 1, foed_dato = 1)
   bef_complete_extra <- tibble(pnr = 1, koen = 1, foed_dato = 1, something = 1)
   bef_incomplete <- tibble(pnr = 1, koen = 1)
 
@@ -22,5 +21,34 @@ test_that("the required variables are present in the dataset", {
   expect_true(verify_required_variables(bef_complete_extra, "bef"))
 
   # When it is a character output, it is a fail
-  expect_character(verify_required_variables(bef_incomplete, "bef"))
+  expect_type(verify_required_variables(bef_incomplete, "bef"), "character")
+})
+
+
+test_that("verification works for DuckDB Database", {
+  actual <- arrow::to_duckdb(bef_complete) |>
+    verify_required_variables("bef")
+
+  expect_true(actual)
+})
+
+test_that("verification works for Arrow Tables (from Parquet)", {
+  actual <- arrow::as_arrow_table(bef_complete) |>
+    verify_required_variables("bef")
+
+  expect_true(actual)
+})
+
+test_that("verification works for data.frame", {
+  actual <- as.data.frame(bef_complete) |>
+    verify_required_variables("bef")
+
+  expect_true(actual)
+})
+
+test_that("verification works for data.table", {
+  actual <- data.table::as.data.table(bef_complete) |>
+    verify_required_variables("bef")
+
+  expect_true(actual)
 })