diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 843c1747..4be5cc8b 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -16,7 +16,6 @@ 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: @@ -33,16 +32,24 @@ jobs: - 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} + # Install Ruby and Jekyll + - name: Setup Ruby + uses: ruby/setup-ruby@v1 + with: + ruby-version: '3.0' # Set this according to your needs + bundler-cache: true + + - name: Install Jekyll + run: bundle install + + - name: Build Jekyll Site + run: bundle exec jekyll build - - name: Deploy to GitHub pages 🚀 + - name: Deploy to GitHub Pages 🚀 if: github.event_name != 'pull_request' uses: JamesIves/github-pages-deploy-action@v4.4.1 with: clean: false branch: gh-pages - folder: docs \ No newline at end of file + folder: _site # Jekyll outputs to the _site folder by default \ No newline at end of file diff --git a/_config.yml b/_config.yml new file mode 100644 index 00000000..fa61d1f3 --- /dev/null +++ b/_config.yml @@ -0,0 +1,3 @@ +remote_theme: pages-themes/minimal@v0.2.0 +plugins: +- jekyll-remote-theme # add this line to the plugins list if you already have one \ No newline at end of file diff --git a/vignettes/model_define.Rmd b/vignettes/model_define.Rmd index ddea411b..b285ccac 100644 --- a/vignettes/model_define.Rmd +++ b/vignettes/model_define.Rmd @@ -214,8 +214,10 @@ Before running the whoel model it is good to check the data and the priors. This p1 <- plotSero(seroModel) p2 <- plotPriorPredictive(seroModel) +p3 <- plotPriorInfection(seroModel) p1 / p2 +p3 ```