Fixed merge conflicts after pull from main

Merge commit '61343b054d2a190eb1e20de6bcb1265c10d2ac34'

#Conflicts:
#	.Rbuildignore
#	DESCRIPTION

.Rbuildignore

@@ -2,3 +2,4 @@
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^data-raw$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,29 @@
+# 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
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2

.github/workflows/pr-commands.yaml

@@ -0,0 +1,79 @@
+# 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: Commands
+
+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 }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$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 }}
+    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 }}

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# 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: test-coverage
+
+jobs:
+  test-coverage:
+    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-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
+inst/doc

DESCRIPTION

@@ -14,15 +14,19 @@ BugReports: https://github.com/steno-aarhus/osdc/issues
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Imports: 
     data.table,
     fs,
     haven,
     here,
+    lifecycle,
     lubridate,
     purrr
-Suggests: 
-    codeCollection,
-    DiagrammeR
-    furrr
+Suggests:
+    codeCollection
+    furrr,
+    DiagrammeR,
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr

R/master.R

@@ -1,81 +0,0 @@
-
-# 0: Master Script for Creating Diabetes Population --------------------------
-
-# Load dependencies:
-library(haven)
-library(data.table)
-library(lubridate)
-library(here)
-library(fs)
-
-# 1: Run Import Script to Convert Raw Files from SAS Format --------
-
-# Set path to root of raw files folder, e.g.:
-foreign_folder = 'E:/ProjektDB/ALMAU/Rawdata/707517/'
-
-# Set names of files to be imported. Can be split across multiple virtual machines for saving time.
-# Executing everything on one machine works fine too.
-
-# To run in 3 simultaneous chuncks on 3 virtual machines, run each of the following sections of 3 lines on a different machine:
-sas_files_1 <- "^bef|^lpr_diag|^uaf_diag|^lpr_adm|^uaf_adm|.*sksube201[4-8]"
-sas_file_list <- list.files(path = foreign_folder, pattern = sas_files_1, recursive = T)
-source(here("R/import.R"))
-
-#
-sas_files_2 <- "^sysi|^sssy200[6-9]|^sssy20[1-9]"
-sas_file_list <- list.files(path = foreign_folder, pattern = sas_files_2, recursive = T)
-source(here("R/import.R"))
-
-#
-sas_files_3 <- "^lab|^lmdb"
-
-sas_files_3 <- "^udda|^akm|^faik"
-sas_file_list <- list.files(path = foreign_folder, pattern = sas_files_3, recursive = T)
-source(here("R/import.R"))
-
-# Set path to root of secondary raw files folder, e.g.:
-foreign_folder = 'E:/ProjektDB/ALMAU/Rawdata/707517/Eksterne data/2021-06-09 fra SDS/'
-sas_files_3 <- "^lab_forsker"
-sas_file_list <- list.files(path = foreign_folder, pattern = sas_files_3, recursive = T)
-source(here("R/import.R"))
-
-
-# Note exclusion of either of sssy and sysi in 2005, where they potentially overlap.
-# Note also that we import medication prescriptions from all years, even though we only filter and use those from 1997 onwards.
-
-
-# 2: Run Filter Script to Create Source Data ---------------------------------
-
-source(here("R/filter.R"))
-
-
-
-# 3: Run Population Script to Generate Diabetes Population -------------------
-source(here("R/population.R"))
-
-
-# 4: Draw a Live Sample of the Diabetes Population at a Point in Time--------------------
-source(here("R/draw_dm_sample.R"))
-
-# Import the entire diabetes population through time:
-dm_population <- readRDS(here('data/output/dm_population.rds'))
-# Select which year to draw the population:
-
-dm_2019 <- draw_dm_sample(sample_year = 2019)
-saveRDS(dm_2019, here("data/output/dm_population_2019.rds"))
-
-rm(dm_population, dm_2018)
-
-# And draw the corresponding diagrams:
-source(here("R/flowcharts.R"))
-load(here("data", "source", "flowchart_counts.Rdata"))
-draw_inclusion()
-draw_type(sample_year = 2019)
-
-
-# 5: Compress Imported Raw Data to Save Space -----------------------------
-
-compress = TRUE
-# Can be set to FALSE if wanting to uncompress the raw data at a later point
-
-source(here("R/compress.R"))

R/osdc-package.R

@@ -0,0 +1,7 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+#' @importFrom lifecycle deprecated
+## usethis namespace: end
+NULL

README.md

@@ -2,14 +2,23 @@
 
 <!-- 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)
+
 <!-- badges: end -->
 
 The goal of *osdc* is to provide an algorithm for classifying diabetes
-within the Danish registers that 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 how 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 will be transparent in the *osdc* repository.
+within the Danish registers that 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 how 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
+will be transparent in the *osdc* repository.
 
 ## Installation
 
@@ -20,3 +29,4 @@ You can install the development version of osdc from
 # install.packages("pak")
 pak::pak("steno-aarhus/osdc")
 ```
+

vignettes/.gitignore

@@ -0,0 +1,2 @@
+*.html
+*.R