diff --git a/.github/workflows/R-CMD-check-dev.yaml b/.github/workflows/R-CMD-check-dev.yaml index b1c4a3f..ae3386e 100644 --- a/.github/workflows/R-CMD-check-dev.yaml +++ b/.github/workflows/R-CMD-check-dev.yaml @@ -1,7 +1,6 @@ +# 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: - - dev pull_request: branches: - dev @@ -10,16 +9,20 @@ name: R-CMD-check-dev jobs: R-CMD-check: - if: "!contains(github.event.head_commit.message, 'skip ci')" - runs-on: macOS-latest + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes steps: - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-r@master - - name: Install dependencies - run: | - install.packages(c("remotes", "rcmdcheck")) - remotes::install_deps(dependencies = TRUE) - shell: Rscript {0} - - name: Check - run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error") - shell: Rscript {0} + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 1b7da60..c8685a7 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,16 +1,15 @@ +# 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: - master - pull_request: - branches: - - master + - dev name: R-CMD-check jobs: R-CMD-check: - if: "!contains(github.event.head_commit.message, 'skip ci')" runs-on: ${{ matrix.config.os }} name: ${{ matrix.config.os }} (${{ matrix.config.r }}) @@ -19,63 +18,32 @@ jobs: fail-fast: false matrix: config: + - {os: macOS-latest, r: 'release'} - {os: windows-latest, r: 'release'} - - {os: macOS-latest, r: 'release'} - - {os: macOS-latest, r: 'devel'} - - {os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - RSPM: ${{ matrix.config.rspm }} + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes steps: - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-r@master + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true - - uses: r-lib/actions/setup-pandoc@master - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Cache R packages - if: runner.os != 'Windows' - uses: actions/cache@v1 + - uses: r-lib/actions/setup-r-dependencies@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 system dependencies - if: runner.os == 'Linux' - env: - RHUB_PLATFORM: linux-x86_64-ubuntu-gcc - run: | - Rscript -e "remotes::install_github('r-hub/sysreqs')" - sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") - sudo -s eval "$sysreqs" - - - name: Install dependencies - run: | - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("rcmdcheck") - shell: Rscript {0} - - - name: Check - env: - _R_CHECK_CRAN_INCOMING_REMOTE_: false - run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") - shell: Rscript {0} + extra-packages: any::rcmdcheck + needs: check - - name: Upload check results - if: failure() - uses: actions/upload-artifact@master + - uses: r-lib/actions/check-r-package@v2 with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check + upload-snapshots: true diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 0ec9d28..46b61eb 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -1,42 +1,46 @@ +# 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: master + pull_request: + branches: [main, master] + release: + types: [published] + workflow_dispatch: name: pkgdown jobs: pkgdown: - runs-on: macOS-latest + 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.GH_TOKEN }} steps: - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-r@master + - uses: r-lib/actions/setup-pandoc@v2 - - uses: r-lib/actions/setup-pandoc@master - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2) - shell: Rscript {0} + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true - - name: Cache R packages - uses: actions/cache@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - path: ${{ env.R_LIBS_USER }} - key: macOS-r-3.6-${{ hashFiles('depends.Rds') }} - restore-keys: macOS-r-3.6- + extra-packages: any::pkgdown, local::. + needs: website - - name: Install dependencies - run: | - install.packages("remotes") - remotes::install_deps(dependencies = TRUE) - remotes::install_dev("pkgdown") + - name: Build site + run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) shell: Rscript {0} - - name: Install package - run: R CMD INSTALL . - - - name: Deploy package - run: pkgdown::deploy_to_branch(new_process = FALSE) - shell: Rscript {0} + - name: Deploy to GitHub pages 🚀 + if: github.event_name != 'pull_request' + uses: JamesIves/github-pages-deploy-action@4.1.4 + with: + clean: false + branch: gh-pages + folder: docs diff --git a/README.Rmd b/README.Rmd index 9842553..9361120 100644 --- a/README.Rmd +++ b/README.Rmd @@ -25,9 +25,7 @@ version <- gsub('-', '.', version) [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) [![packageversion](https://img.shields.io/badge/package%20version-`r version`-orange.svg)](https://github.com/abichat/evabic/blob/master/DESCRIPTION) [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/evabic)](https://cran.r-project.org/package=evabic) -[![Codecov test coverage](https://codecov.io/gh/abichat/evabic/branch/master/graph/badge.svg)](https://codecov.io/gh/abichat/evabic?branch=master) -[![Codacy Badge](https://api.codacy.com/project/badge/Grade/c32dcc4c1c3f40a5950e1c10ea6dfb18)](https://www.codacy.com/app/abichat/evabic?utm_source=github.com&utm_medium=referral&utm_content=abichat/evabic&utm_campaign=Badge_Grade) -[![R build status](https://github.com/abichat/evabic/workflows/R-CMD-check/badge.svg)](https://github.com/abichat/evabic/actions) +[![R-CMD-check](https://github.com/abichat/evabic/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/abichat/evabic/actions/workflows/R-CMD-check.yaml) [![Documentation](https://img.shields.io/badge/documentation-pkgdown-E91E63.svg)](https://abichat.github.io/evabic/) [![last-commit](https://img.shields.io/github/last-commit/abichat/evabic.svg)](https://github.com/abichat/evabic/commits/master) diff --git a/README.md b/README.md index 351ef2b..0707c88 100644 --- a/README.md +++ b/README.md @@ -9,12 +9,7 @@ [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) [![packageversion](https://img.shields.io/badge/package%20version-0.0.4.9000-orange.svg)](https://github.com/abichat/evabic/blob/master/DESCRIPTION) [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/evabic)](https://cran.r-project.org/package=evabic) -[![Codecov test -coverage](https://codecov.io/gh/abichat/evabic/branch/master/graph/badge.svg)](https://codecov.io/gh/abichat/evabic?branch=master) -[![Codacy -Badge](https://api.codacy.com/project/badge/Grade/c32dcc4c1c3f40a5950e1c10ea6dfb18)](https://www.codacy.com/app/abichat/evabic?utm_source=github.com&utm_medium=referral&utm_content=abichat/evabic&utm_campaign=Badge_Grade) -[![R build -status](https://github.com/abichat/evabic/workflows/R-CMD-check/badge.svg)](https://github.com/abichat/evabic/actions) +[![R-CMD-check](https://github.com/abichat/evabic/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/abichat/evabic/actions/workflows/R-CMD-check.yaml) [![Documentation](https://img.shields.io/badge/documentation-pkgdown-E91E63.svg)](https://abichat.github.io/evabic/) [![last-commit](https://img.shields.io/github/last-commit/abichat/evabic.svg)](https://github.com/abichat/evabic/commits/master) @@ -44,8 +39,8 @@ False Discovery Rate, Accuracy, F1… ``` r evabic::ebc_allmeasures -#> [1] "TP" "FP" "FN" "TN" "TPR" "TNR" "PPV" "NPV" "FNR" "FPR" "FDR" -#> [12] "FOR" "ACC" "BACC" "F1" "PLR" "NLR" "DOR" +#> [1] "TP" "FP" "FN" "TN" "TPR" "TNR" "PPV" "NPV" "FNR" "FPR" +#> [11] "FDR" "FOR" "ACC" "BACC" "F1" "PLR" "NLR" "DOR" ``` All measures are computed from the confusion matrix: @@ -114,8 +109,10 @@ summary(model) #> F-statistic: 69.99 on 7 and 42 DF, p-value: < 2.2e-16 pvalues <- summary(model)$coefficients[-1, 4] pvalues -#> X1 X2 X3 X4 X5 X6 X7 -#> 0.004366456 0.829771754 0.003469737 0.491828466 0.581608670 0.887948400 0.449664443 +#> X1 X2 X3 X4 X5 X6 +#> 0.004366456 0.829771754 0.003469737 0.491828466 0.581608670 0.887948400 +#> X7 +#> 0.449664443 detected_var <- names(pvalues[pvalues < 0.05]) detected_var #> [1] "X1" "X3"