diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index a3ac618..14159b7 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.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")' diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml new file mode 100644 index 0000000..a7276e8 --- /dev/null +++ b/.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/github-pages-deploy-action@v4.5.0 + with: + clean: false + branch: gh-pages + folder: docs diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 2c5bb50..21b8a93 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.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: @@ -31,7 +31,7 @@ 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} @@ -39,12 +39,12 @@ jobs: 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 diff --git a/.gitignore b/.gitignore index 7487699..25718fe 100644 --- a/.gitignore +++ b/.gitignore @@ -4,3 +4,4 @@ .Ruserdata .DS_Store inst/doc +docs diff --git a/DESCRIPTION b/DESCRIPTION index 962de90..5d4fdb1 100644 --- a/DESCRIPTION +++ b/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 diff --git a/README.Rmd b/README.Rmd index fb4d17c..d93545a 100644 --- a/README.Rmd +++ b/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? diff --git a/README.md b/README.md index a54c777..ee59ce0 100644 --- a/README.md +++ b/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 diff --git a/man/sleacr.Rd b/man/sleacr.Rd index 69195c7..1731d1b 100644 --- a/man/sleacr.Rd +++ b/man/sleacr.Rd @@ -2,8 +2,8 @@ % Please edit documentation in R/sleacr.R \docType{package} \name{sleacr} -\alias{sleacr} \alias{sleacr-package} +\alias{sleacr} \title{sleacr: Simplified Lot Quality Assurance Sampling Evaluation of Access and Coverage (SLEAC) Tools in R} \description{ \if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}} @@ -18,8 +18,7 @@ Access and Coverage (SLEAC) Technical Reference. Washington, DC: FHI 360/FANTA. \seealso{ Useful links: \itemize{ - \item \url{https://nutriverse.io/sleacr/} - \item \url{https://github.com/nutriverse/sleacr} + \item \url{https://nutriverse.io/sleacr/,https://github.com/nutriverse/sleacr} \item Report bugs at \url{https://github.com/nutriverse/sleacr/issues} } diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml index eee4f56..f9e57c9 100644 --- a/pkgdown/_pkgdown.yml +++ b/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