Merge pull request #28 from nutriverse/dev

update documentation

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

@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -47,3 +47,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.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

.github/workflows/test-coverage.yaml

@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -31,20 +31,20 @@ jobs:
           covr::codecov(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
         shell: Rscript {0}
 
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

.gitignore

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

DESCRIPTION

@@ -32,9 +32,9 @@ Suggests:
 Encoding: UTF-8
 Language: en-GB
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
-URL: https://nutriverse.io/sleacr/, https://github.com/nutriverse/sleacr
+URL: https://nutriverse.io/sleacr/,https://github.com/nutriverse/sleacr
 BugReports: https://github.com/nutriverse/sleacr/issues
 Config/testthat/edition: 3
 VignetteBuilder: knitr

README.Rmd

@@ -29,11 +29,13 @@ In the recent past, measurement of coverage has been mainly through two-stage cl
 
 ## Installation
 
-The `sleacr` package is not yet available on [CRAN](https://cran.r-project.org). You can install the development version of `sleacr` from [GitHub](https://github.com/nutriverse/sleacr) with:
+The `sleacr` package is not yet available on [CRAN](https://cran.r-project.org) but can be installed from the [Nutriverse R universe](https://nutriverse.r-universe.dev) as follows:
 
-``` r
-if (!require(remotes)) install.packages("remotes")
-remotes::install_github("nutriverse/sleacr")
+```{r install, echo = TRUE, eval = FALSE}
+install.packages(
+  "sleacr",
+  repos = c('https://nutriverse.r-universe.dev', 'https://cloud.r-project.org')
+)
 ```
 
 ## What does `sleacr` do?

README.md

@@ -34,13 +34,14 @@ functions for use in conducting a SLEAC assessment.
 ## Installation
 
 The `sleacr` package is not yet available on
-[CRAN](https://cran.r-project.org). You can install the development
-version of `sleacr` from [GitHub](https://github.com/nutriverse/sleacr)
-with:
+[CRAN](https://cran.r-project.org) but can be installed from the
+[Nutriverse R universe](https://nutriverse.r-universe.dev) as follows:
 
 ``` r
-if (!require(remotes)) install.packages("remotes")
-remotes::install_github("nutriverse/sleacr")
+install.packages(
+  "sleacr",
+  repos = c('https://nutriverse.r-universe.dev', 'https://cloud.r-project.org')
+)
 ```
 
 ## What does `sleacr` do?
@@ -64,7 +65,6 @@ citation provided by a call to the `citation` function as follows:
 
 ``` r
 citation("sleacr")
-#> 
 #> To cite sleacr in publications use:
 #> 
 #>   Ernest Guevarra (2023). sleacr: Simplified Lot Quality Assurance

pkgdown/_pkgdown.yml

@@ -1,72 +1,70 @@
 title: sleacr
 
-url: https://nutriverse.io/sleacr
+url: https://nutriverse.io/sleacr/
 
 template:
   bootstrap: 5
-  bootswatch: lumen
+  bootswatch: cosmo
   theme: haddock
   ganalytics: UA-102485058-6
 
 navbar:
-  bg: primary
+  bg: success
   type: light
   structure:
-    left:  [home, intro, reference, articles, news]
-    right: [twitter, linkedin, github]
-
+    left:
+    - home
+    - intro
+    - reference
+    - articles
+    - news
+    right:
+    - mastodon
+    - linkedin
+    - github
   components:
-    # articles:
-    #   text: Articles
-    #   menu:
-    #   - text: "Detecting haemoglobinaemia"
-    #     href: articles/haemoglobinaemia.html
-    twitter:
-      icon: "fab fa-twitter fa-lg"
-      href: https://twitter.com/katilingban
+    mastodon:
+      icon: fab fa-mastodon fa-lg
+      href: https://fosstodon.org/@katilingban
     linkedin:
-      icon: "fab fa-linkedin fa-lg"
+      icon: fab fa-linkedin fa-lg
       href: https://www.linkedin.com/company/katilingban
 
 home:
-  #strip_header: true
   links:
-  - text: Read more about Simplified Lot Quality Assurance Sampling Evaluation of Access and Coverage (SLEAC)
+  - text: Read more about Simplified Lot Quality Assurance Sampling Evaluation of
+      Access and Coverage (SLEAC)
     href: https://www.fantaproject.org/sites/default/files/resources/SQUEAC-SLEAC-Technical-Reference-Oct2012_0.pdf
 
 reference:
-  - title: Sample size estimation
-    contents:
-    - get_binom_hypergeom
-    - get_hypergeom
-    - get_hypergeom_cumulative
-    - get_n
-    - get_d
-    - get_n_cases
-    - get_n_clusters
-
-  - title: Stage 1 sampling
-    contents:
-    - get_sampling_interval
-    - select_random_start
-    - select_sampling_clusters
-    - create_sampling_list
-
-  - title: Coverage classifier
-    contents:
-    - classify_coverage
-
-  - title: Tests for SLEAC classifier performance
-    contents:
-    - make_data
-    - run_lqas
-    - simulate_lqas
-    - test_lqas_classifier
-    - get_class_prob
-    - print.lqasClass
-    - plot.lqasSim
+- title: Sample size estimation
+  contents:
+  - get_binom_hypergeom
+  - get_hypergeom
+  - get_hypergeom_cumulative
+  - get_n
+  - get_d
+  - get_n_cases
+  - get_n_clusters
+- title: Stage 1 sampling
+  contents:
+  - get_sampling_interval
+  - select_random_start
+  - select_sampling_clusters
+  - create_sampling_list
+- title: Coverage classifier
+  contents: classify_coverage
+- title: Tests for SLEAC classifier performance
+  contents:
+  - make_data
+  - run_lqas
+  - simulate_lqas
+  - test_lqas_classifier
+  - get_class_prob
+  - print.lqasClass
+  - plot.lqasSim
+- title: Datasets
+  contents:
+  - village_list
+  - survey_data
 
-  - title: Datasets
-    contents:
-    - village_list
-    - survey_data