Refactor R functions, enhance README, and update documentation

.Rbuildignore

@@ -1,2 +1,20 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^\.travis\.yml$
+^README\.Rmd$
+^_pkgdown\.yml$
+^\.github$
+^_gitignore$
+^\.gitlab-ci\.yml$
+^_Rbuildignore$
+^\.gitignore$
+^LICENSE\.md$
+^README\.md$
+^drc_3\.3\.0\.tar\.gz$
+^drc_.*\.tar\.gz$
+^news$
+^docs$
+^local_testing$
+^\.vscode$
+^build_pkgdown\.R$
+^CITATION\.cff$

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

@@ -0,0 +1,56 @@
+# 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, main_beta, dev]
+  pull_request:
+    branches: [main, main_beta, dev]
+
+name: R-CMD-check
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        env:
+          PKG_CPPFLAGS: ${{ matrix.config.r == 'devel' && '-DPREXPR=PRCODE' || '' }}
+        with:
+          extra-packages: |
+            any::rcmdcheck
+            ${{ matrix.config.r == 'devel' && 'r-lib/rlang' || '' }}
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/static.yml

@@ -0,0 +1,45 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy static content to Pages
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["dev"]
+    paths:
+      - 'docs/**'
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Single deploy job since we're just deploying
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+      - name: Setup Pages
+        uses: actions/configure-pages@v5
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          # Upload docs directory where pkgdown builds the site
+          path: 'docs'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/test-coverage.yaml

@@ -0,0 +1,69 @@
+# 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, main_beta, dev]
+    paths:
+      - 'tests/**'
+      - 'R/**'
+  pull_request:
+    branches: [main, main_beta, dev]
+    paths:
+      - 'tests/**'
+      - 'R/**'
+
+name: test-coverage
+
+permissions: read-all
+
+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, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ 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

@@ -1,4 +1,56 @@
+# R session files
 .Rproj.user
 .Rhistory
 .RData
 .Ruserdata
+
+# R package build artifacts
+*.tar.gz
+*.tgz
+*.zip
+*.7z
+*.Rcheck/
+*.Rproj
+README.Rmd
+/pkgdown/
+pkgdown/*
+
+# Caching
+.Rinst
+.Rlibs
+*~
+*.o
+*.so
+*.dll
+
+# Local test repositories
+local_testing/*
+
+# knitr / RMarkdown cache
+*_cache/
+/cache/
+
+# OAuth token
+.httr-oauth
+
+# Tests output
+tests/testthat/_snaps/
+Rplots.pdf
+tests/testthat/Rplots.pdf
+
+# OS-generated files
+.DS_Store
+Thumbs.db
+
+# R environment files
+.Renviron
+
+# Quarto
+.quarto/
+
+# Reference/backup files
+_gitignore
+_Rbuildignore
+
+# YAML Package build tests and artifacts
+/docs_old/

CITATION.cff

@@ -0,0 +1,55 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Reinwald"
+  given-names: "Hannes"
+  orcid: "https://orcid.org/0000-0003-3133-679X"
+- family-names: "Ritz"
+  given-names: "Christian"
+  orcid: "https://orcid.org/0000-0002-5095-0624"
+- family-names: "Baty"
+  given-names: "Florent"
+  orcid: "https://orcid.org/0000-0002-1425-0428"
+- family-names: "Streibig"
+  given-names: "Jens Carl"
+  orcid: "https://orcid.org/0000-0002-6204-4004"
+- family-names: "Gerhard"
+  given-names: "Daniel"
+  orcid: "https://orcid.org/0000-0002-9336-3454"
+title: "Dose-Response Analysis Using R"
+version: 3.3.2
+doi: 10.1371/journal.pone.0146021
+date-released: 2015-12-15
+url: "https://github.com/hreinwald/drc"
+references:
+  - type: article
+    title: "Dose-Response Analysis Using R"
+    authors:
+      - family-names: "Ritz"
+        given-names: "Christian"
+      - family-names: "Baty"
+        given-names: "Florent"
+      - family-names: "Streibig"
+        given-names: "Jens C"
+      - family-names: "Gerhard"
+        given-names: "Daniel"
+    journal: "PLoS ONE"
+    volume: 10
+    issue: 12
+    pages: "e0146021"
+    year: 2015
+    doi: "10.1371/journal.pone.0146021"
+  - type: book
+    title: "Dose-Response Analysis Using R"
+    authors:
+      - family-names: "Ritz"
+        given-names: "C."
+      - family-names: "Jensen"
+        given-names: "S. M."
+      - family-names: "Gerhard"
+        given-names: "D."
+      - family-names: "Streibig"
+        given-names: "J. C."
+    publisher:
+      name: "CRC Press"
+    year: 2019

DESCRIPTION

@@ -1,16 +1,25 @@
 Package: drc
-Version: 3.2-0
-Date: 2021-01-13
+Version: 3.3.2
+Date: 2026-05-22
 Title: Analysis of Dose-Response Data
-Authors@R: c(person("Christian" , "Ritz", role = c("aut", "cre"), email="ritz@bioassay.dk"), 
-             person("Jens", "Streibig", middle="C.", email="streibig@bioassay.dk", role = "aut"))
-Maintainer: Christian Ritz <ritz@bioassay.dk>
-Depends: R (>= 2.0.0), MASS, stats, drcData
-Imports: car, gtools, multcomp, plotrix, sandwich, scales
-LazyLoad: yes
+Authors@R: c(person("Christian", "Ritz", role = c("aut"), email = "ritz@bioassay.dk"),
+             person(c("Jens", "C."), "Streibig", email = "streibig@bioassay.dk", role = "aut"),
+             person("Hannes", "Reinwald", email = "hannes.reinwald@bayer.com", role = c("aut", "cre")))
+Depends: R (>= 4.0.0), MASS, stats
+Imports: car, data.table, dplyr, graphics, gtools, multcomp, plotrix, sandwich, scales, utils, lifecycle
+Encoding: UTF-8
 LazyData: yes
-Description: Analysis of dose-response data is made available through a suite of flexible and versatile model fitting and after-fitting functions.
-License: GPL-2
-URL: http://www.r-project.org, http://www.bioassay.dk
-RoxygenNote: 6.1.1
-BugReports: https://github.com/DoseResponse/drc/issues/
+Description: Analysis of dose-response data is made available through a suite of
+    flexible and versatile model fitting and after-fitting functions.
+License: GPL-2 | file LICENSE
+URL: https://hreinwald.github.io/drc, https://github.com/hreinwald/drc, https://www.bioassay.dk, https://www.r-project.org, https://cran.r-project.org/web/packages/drc/index.html
+RoxygenNote: 7.3.3
+BugReports: https://github.com/hreinwald/drc/issues/
+Roxygen: list(markdown = TRUE)
+Suggests:
+    testthat (>= 3.0.0),
+    knitr,
+    magic,
+    rmarkdown
+VignetteBuilder: knitr
+Config/testthat/edition: 3