Merge pull request #43 from nutriverse/vignettes

Vignettes

Author: tomaszaba

.Rbuildignore

@@ -10,3 +10,9 @@
 ^doc$
 ^Meta$
 ^data-raw$
+^README\.qmd$
+^README_files$
+^mwana\.Rproj$
+^vignettes/plausibility_files$
+^vignettes/prevalence_files$
+^vignettes/sample_size_files$

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

@@ -31,6 +31,13 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - uses: quarto-dev/quarto-actions/setup@v2
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          version: ${{ matrix.config.quarto || 'release' }}
+          tinytex: true
+
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
@@ -41,7 +48,8 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          # install the package itself as we register vignette engine
+          extra-packages: any::rcmdcheck, local::.
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2

.github/workflows/pkgdown.yaml

@@ -0,0 +1,53 @@
+# 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.yaml
+
+permissions: read-all
+
+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
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - 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/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/pr-commands.yaml

@@ -13,6 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/test-coverage.yaml

@@ -9,3 +9,11 @@ inst/doc
 docs
 /doc/
 /Meta/
+
+/README_files/
+
+/vignettes/plausibility_files/
+/vignettes/prevalence_files/
+/vignettes/sample_size_files/
+
+/.quarto/

.gitignore

@@ -15,7 +15,6 @@ Description: A streamlined and comprehensive implementation of the Standardized
   handling large multiple datasets.
 License: GPL (>= 3)
 URL: https://github.com/nutriverse/mwana, https://nutriverse.io/mwana
-BugReports: https://github.com/nutriverse/mwana/issues
 Imports: 
     dplyr (>= 1.1.4),
     lubridate,
@@ -29,6 +28,7 @@ Imports:
 Suggests:
     knitr,
     rmarkdown,
+    quarto,
     spelling,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
@@ -39,4 +39,4 @@ RoxygenNote: 7.3.2
 Depends: 
     R (>= 4.1)
 LazyData: true
-VignetteBuilder: knitr
+VignetteBuilder: quarto

DESCRIPTION

@@ -38,10 +38,10 @@ compute_age_in_months <- function (surv_date, birth_date) {
 
 
 #'
-#' Wrangle child's age
+#' Process child's age
 #'
 #' @description
-#' Wrangle child's age for downstream analysis. This includes calculating age
+#' Process child's age for downstream analysis. This includes calculating age
 #' in months based on the date of data collection and child's date of birth and
 #' setting to `NA` the age values that are less than 6.0 and greater than or equal
 #' to 60.0 months old.
@@ -66,6 +66,7 @@ compute_age_in_months <- function (surv_date, birth_date) {
 #' @examples
 #'
 #' ## A sample data ----
+#'
 #' df <- data.frame(
 #' survy_date = as.Date(c(
 #' "2023-01-01", "2023-01-01", "2023-01-01", "2023-01-01", "2023-01-01")),