Merge pull request #31 from steno-aarhus/build/setup-package

.Rbuildignore

@@ -2,3 +2,7 @@
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^\.github$
+^CODE_OF_CONDUCT\.md$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/CODEOWNERS

@@ -0,0 +1,2 @@
+# Request reviews from each person for Pull Requests on any file
+* @Aastedet @lwjohnst86 @signekb

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

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

CODE_OF_CONDUCT.md

@@ -0,0 +1,126 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at [email protected]. 
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
+
+[homepage]: https://www.contributor-covenant.org

DESCRIPTION

@@ -2,14 +2,21 @@ Type: Package
 Package: osdc
 Title: Open Source Diabetes Classifier for Danish Registers.
 Version: 0.0.1.9000
-Authors@R: 
-    person("Anders", "Isaksen", , "[email protected]", role = c("cre", "aut"))
+Authors@R: c(
+    # cre = maintainer, even though it translates to "creator"
+    person(c("Luke", "William"), "Johnston", , "[email protected]",
+           comment = c(ORCID = "0000-0003-4169-2616"), role = c("aut", "cre")),
+    person(c("Signe", "Kirk"), "Brødbæk", , "[email protected]", role = "aut"),
+    person(c("Anders", "Aasted"), "Isaksen", , "[email protected]", role = "aut"),
+    person("Steno Diabetes Center Aarhus", role = "cph"),
+    person("Aarhus University", role = "cph")
+  )
 Description: This classifier first identifies a population of individuals
     with any type of diabetes mellitus and then splits this population
     into T1D and T2D by identifying individuals with T1D and classifying
     the remainder of the diabetes population as T2D.
 License: MIT + file LICENSE
-URL: https://github.com/steno-aarhus/osdc
+URL: https://github.com/steno-aarhus/osdc, https://steno-aarhus.github.io/osdc/
 BugReports: https://github.com/steno-aarhus/osdc/issues
 Encoding: UTF-8
 LazyData: true
@@ -27,5 +34,9 @@ Suggests:
     furrr,
     DiagrammeR,
     knitr,
-    rmarkdown
+    rmarkdown,
+    spelling,
+    testthat (>= 3.0.0)
 VignetteBuilder: knitr
+Language: en-US
+Config/testthat/edition: 3

LICENSE.md

@@ -1,21 +1,23 @@
 # MIT License
 
-Copyright (c) 2022-2023 Anders Aasted Isaksen
+Copyright (c) 2022-2023 Steno Diabetes Center Aarhus and Aarhus
+University
 
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+Permission is hereby granted, free of charge, to any person obtaining a
+copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
 
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
+The above copyright notice and this permission notice shall be included
+in all copies or substantial portions of the Software.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

NEWS.md

@@ -0,0 +1 @@
+# osdc (development version)

README.md

@@ -30,3 +30,10 @@ You can install the development version of osdc from
 pak::pak("steno-aarhus/osdc")
 ```
 
+## Code of Conduct
+
+Please note that the osdc project is released with a [Contributor Code
+of
+Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html).
+By contributing to this project, you agree to abide by its terms.
+

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: https://steno-aarhus.github.io/osdc/
+template:
+  bootstrap: 5
+

inst/WORDLIST

@@ -0,0 +1,5 @@
+CMD
+DuckDB
+Stata
+dplyr
+mellitus

osdc.Rproj

@@ -20,6 +20,8 @@ PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
 PackageRoxygenize: rd,collate,namespace
 
+UseNativePipeOperator: Yes
+
 MarkdownWrap: Column
 MarkdownWrapAtColumn: 72
 MarkdownCanonical: Yes

tests/spelling.R

@@ -0,0 +1,3 @@
+if(requireNamespace('spelling', quietly = TRUE))
+  spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                             skip_on_cran = TRUE)

tests/testthat.R

@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(osdc)
+
+test_check("osdc")

vignettes/design.Rmd

@@ -0,0 +1,15 @@
+---
+title: "Design"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{design}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```