skeleton

.Rbuildignore

@@ -0,0 +1,4 @@
+^template\.Rproj$
+^\.Rproj\.user$
+^LICENSE\.md$
+^\.github$

.github/.gitignore

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

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

@@ -0,0 +1,83 @@
+# ===================================================================== #
+#  An R package by Certe:                                               #
+#  https://github.com/certe-medical-epidemiology                        #
+#                                                                       #
+#  Licensed as GPL-v2.0.                                                #
+#                                                                       #
+#  Developed at non-profit organisation Certe Medical Diagnostics &     #
+#  Advice, department of Medical Epidemiology.                          #
+#                                                                       #
+#  This R package is free software; you can freely use and distribute   #
+#  it for both personal and commercial purposes under the terms of the  #
+#  GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+#  the Free Software Foundation.                                        #
+#                                                                       #
+#  We created this package for both routine data analysis and academic  #
+#  research and it was publicly released in the hope that it will be    #
+#  useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+# ===================================================================== #
+
+# Remember that R-universe will hourly build binaries for macOS and Windows:
+# https://certe-medical-epidemiology.r-universe.dev
+
+on:
+  push:
+    branches: main
+  pull_request:
+    branches: main
+  schedule:
+    # run a schedule everyday at 1 AM.
+    # this is to check that all dependencies are still available
+    - cron:  '0 1 * * *'
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    continue-on-error: ${{ matrix.config.allowfail }}
+    name: ${{ matrix.config.os }} (R-${{ matrix.config.r }})
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'devel',   allowfail: true}
+          - {os: macOS-latest,   r: '4.1',     allowfail: false}
+          - {os: macOS-latest,   r: '4.0',     allowfail: false}
+          - {os: macOS-latest,   r: '3.6',     allowfail: false}
+          - {os: ubuntu-20.04,   r: 'devel',   allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: '4.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: '4.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: '3.6',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: windows-latest, r: 'devel',   allowfail: true}
+          - {os: windows-latest, r: '4.1',     allowfail: false}
+          - {os: windows-latest, r: '4.0',     allowfail: false}
+          - {os: windows-latest, r: '3.6',     allowfail: false}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: rcmdcheck
+
+      - uses: r-lib/actions/check-r-package@v1
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/lintr.yaml

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+# ===================================================================== #
+#  An R package by Certe:                                               #
+#  https://github.com/certe-medical-epidemiology                        #
+#                                                                       #
+#  Licensed as GPL-v2.0.                                                #
+#                                                                       #
+#  Developed at non-profit organisation Certe Medical Diagnostics &     #
+#  Advice, department of Medical Epidemiology.                          #
+#                                                                       #
+#  This R package is free software; you can freely use and distribute   #
+#  it for both personal and commercial purposes under the terms of the  #
+#  GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+#  the Free Software Foundation.                                        #
+#                                                                       #
+#  We created this package for both routine data analysis and academic  #
+#  research and it was publicly released in the hope that it will be    #
+#  useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+# ===================================================================== #
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+name: lintr
+
+jobs:
+  lintr:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("lintr")
+        shell: Rscript {0}
+
+      - name: Lint
+        run: lintr::lint_package(linters = lintr::with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_length_linter = lintr::object_length_linter(length = 50L)))
+        shell: Rscript {0}

.gitignore

@@ -19,6 +19,7 @@
 
 # RStudio files
 .Rproj.user/
+template.Rproj
 
 # produced vignettes
 vignettes/*.html
@@ -35,5 +36,10 @@ vignettes/*.pdf
 *.utf8.md
 *.knit.md
 
+# Temporary files created by OS
+.DS_Store
+Thumbs.db
+
 # R Environment Variables
 .Renviron
+.Rproj.user

DESCRIPTION

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+Package: certetemplate
+Title: A Certe Package for ...
+Version: 0.0.1.9000
+Authors@R: c(
+  person(given = c("Matthijs", "S."), 
+         family = "Berends",
+         role = c("aut", "cre")),
+  person(given = c("Erwin", "E.", "A."),
+         family = "Hassing", 
+         role = c("aut")),
+  person(given = c("Erwin"),
+         family = "Dijkstra", 
+         role = c("aut")),
+  person(given = "Certe Medical Diagnostics & Advice Foundation",
+         role = c("cph", "fnd")))
+Description: A Certe R Package for ... .
+  This package is part of the 'certedata' universe.
+URL: https://github.com/certe-medical-epidemiology
+Depends: 
+    R (>= 3.6.0)
+Suggests: 
+    testthat (>= 2.0.0)
+License: GPL-2
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.2
+Config/testthat/edition: 2