diff --git a/.github/workflows/check-url-2.yml b/.github/workflows/check-url-2.yml
new file mode 100644
index 0000000..1ff5987
--- /dev/null
+++ b/.github/workflows/check-url-2.yml
@@ -0,0 +1,121 @@
+name: Periodic URL Check 2
+
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 0 1 * *'
+
+jobs:
+  set-up:
+    name: Load user automation choices
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+        # Use the yaml-env-action action.
+      - name: Load environment from YAML
+        uses: doughepi/yaml-env-action@v1.0.0
+        with:
+            files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
+    outputs:
+      toggle_url_check_periodically: "${{ env.URL_CHECK_PERIODICALLY }}"
+
+  url-check:
+    name: Check URLs
+    needs: set-up
+    if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'true'}}
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+
+    # Delete the branch if this has been run before
+    - name: Delete branch locally and remotely
+      run: git push origin --delete preview-spell-error || echo "No branch to delete"
+
+    # Make the branch fresh
+    - name: Make the branch fresh
+      run: |
+        git config --global --add safe.directory $GITHUB_WORKSPACE
+        git config --global user.name 'github-actions[bot]'
+        git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+
+        echo branch doesnt exist
+        git checkout -b preview-spell-error || echo branch exists
+        git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
+      shell: bash
+
+    - name: Run the check
+      uses: ottrproject/ottr-reports@main
+      id: check_results
+      continue-on-error: true
+      with:
+        check_spelling: false
+        spelling_error_min: 1
+        check_urls: true
+        url_error_min: 1
+        check_quiz_form: false
+        quiz_error_min: 1
+        sort_dictionary: false
+
+    - name: Declare file path and time
+      id: check-report
+      run: |
+        error_num=$(cat check_reports/url_checks.tsv | wc -l)
+        error_num="$((error_num-1))"
+        echo "error_num=$error_num" >> $GITHUB_OUTPUT
+        echo "error_url=https://github.com/${GITHUB_REPOSITORY}/blob/preview-spell-error/check_reports/url_checks.tsv" >> $GITHUB_OUTPUT
+      shell: bash
+
+    - name: Stop if failure
+      if: steps.check_results.outcome == 'failure'
+      run: exit 1
+
+    - name: Print out error variables
+      run: |
+        echo ${{ steps.check-report.outputs.error_url }}
+        echo ${{ steps.check-report.outputs.error_num }}
+
+      # Commit file
+    - name: Commit tocless bookdown files
+      if: ${{ steps.check-report.outputs.error_num >= 1 }}
+      env:
+        GH_PAT: ${{ secrets.GH_PAT }}
+      run: |
+        git add --force check_reports/url_checks.tsv
+        git commit -m 'Add spell check file' || echo "No changes to commit"
+        git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
+
+    - name: Find issues
+      id: find-issue
+      env:
+        GH_PAT: ${{ secrets.GH_PAT }}
+      run: |
+        echo "$GITHUB_REPOSITORY"
+        curl -o find_issue.R https://raw.githubusercontent.com/ottrproject/ottr-reports/main/scripts/find_issue.R
+        issue_exists=$(Rscript --vanilla find_issue.R --repo $GITHUB_REPOSITORY --git_pat $GH_PAT)
+        echo URL issue exists: $issue_exists
+        echo "issue_existence=$issue_exists" >> $GITHUB_OUTPUT
+
+    - name: If too many URL errors, then make an issue
+      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_existence == 0}}
+      uses: JasonEtco/create-an-issue@v2
+      with:
+        filename: .github/ISSUE_TEMPLATE/url-error.md
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        FILE_URL: ${{ steps.check-report.outputs.error_url }}
+        ERROR_NUM: ${{ steps.check-report.outputs.error_num }}
+
+    - name: If no URL errors than delete the branch we made
+      if: ${{ steps.check-report.outputs.error_num < 1 }}
+      run: |
+        git config --system --add safe.directory "$GITHUB_WORKSPACE"
+        git push origin --delete preview-spell-error || echo "No branch to delete"
diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
index 090f12f..6cfef1a 100644
--- a/.github/workflows/check-url.yml
+++ b/.github/workflows/check-url.yml
@@ -26,7 +26,7 @@ jobs:
   url-check:
     name: Check URLs
     needs: set-up
-    if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'yes'}}
+    if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'true'}}
     runs-on: ubuntu-latest
     container:
       image: jhudsl/base_ottr:main
@@ -54,12 +54,17 @@ jobs:
       shell: bash
 
     - name: Run the check
-      uses: jhudsl/ottr-reports@main
+      uses: ottrproject/ottr-reports@main
       id: check_results
       continue-on-error: true
       with:
-        check_type: urls
-        error_min: 1
+        check_spelling: false
+        spelling_error_min: 1
+        check_urls: true
+        url_error_min: 1
+        check_quiz_form: false
+        quiz_error_min: 1
+        sort_dictionary: false
 
     - name: Declare file path and time
       id: check-report
@@ -78,7 +83,7 @@ jobs:
       run: |
         echo ${{ steps.check-report.outputs.error_url }}
         echo ${{ steps.check-report.outputs.error_num }}
-        
+
       # Commit file
     - name: Commit tocless bookdown files
       if: ${{ steps.check-report.outputs.error_num >= 1 }}
@@ -95,7 +100,7 @@ jobs:
         GH_PAT: ${{ secrets.GH_PAT }}
       run: |
         echo "$GITHUB_REPOSITORY"
-        curl -o find_issue.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/find_issue.R
+        curl -o find_issue.R https://raw.githubusercontent.com/ottrproject/ottr-reports/main/scripts/find_issue.R
         issue_exists=$(Rscript --vanilla find_issue.R --repo $GITHUB_REPOSITORY --git_pat $GH_PAT)
         echo URL issue exists: $issue_exists
         echo "issue_existence=$issue_exists" >> $GITHUB_OUTPUT
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 091af95..9b3ece7 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -1,5 +1,5 @@
 # Candace Savonen 2021
-# Updated May 2024
+# Updated May 2025
 
 name: Pull Request
 
@@ -45,57 +45,51 @@ jobs:
     outputs:
       toggle_website: "${{ env.RENDER_WEBSITE }}"
       toggle_spell_check: "${{ env.SPELL_CHECK }}"
+      spell_error_min: "${{ env.SPELL_ERROR_MIN }}"
       toggle_style_code: "${{ env.STYLE_CODE }}"
       toggle_url_check: "${{ env.URL_CHECKER }}"
+      url_error_min: "${{ env.URL_ERROR_MIN }}"
       toggle_quiz_check: "${{ env.CHECK_QUIZZES }}"
+      quiz_error_min: "${{ env.QUIZ_ERROR_MIN }}"
       toggle_md_linter: "${{ env.MARKDOWN_LINTER }}"
       toggle_readability: "${{ env.READABILITY_REPORT }}"
       toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
+      toggle_dictionary_sort: "${{ env.DICTIONARY_SORT }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
 
 ########################## Make the error reports ##############################
-  spell-check:
-    name: Check spelling
+  ottr-reports:
+    name: Run Reports
     needs: yaml-check
-    if: ${{needs.yaml-check.outputs.toggle_spell_check == 'yes'}}
-    uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
-    with:
-      check_type: spelling
-      error_min: 3
-      branch_name: ${GITHUB_HEAD_REF}
-    secrets:
-      gh_pat: ${{ secrets.GH_PAT }}
-
-  url-check:
-    name: Check URLs
-    needs: yaml-check
-    if: ${{needs.yaml-check.outputs.toggle_url_check == 'yes'}}
-    uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
-    with:
-      check_type: urls
-      error_min: 0
-      branch_name: ${GITHUB_HEAD_REF}
-    secrets:
-      gh_pat: ${{ secrets.GH_PAT }}
+    if: ${{needs.yaml-check.outputs.toggle_spell_check == 'true' || needs.yaml-check.outputs.toggle_url_check == 'true' || needs.yaml-check.outputs.toggle_quiz_check == 'true'}}
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
 
-  quiz-check:
-    name: Check quiz formatting
-    if: ${{needs.yaml-check.outputs.toggle_quiz_check == 'yes'}}
-    needs: yaml-check
-    uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
-    with:
-      check_type: quiz_format
-      error_min: 0
-      branch_name: ${GITHUB_HEAD_REF}
-    secrets:
-      gh_pat: ${{ secrets.GH_PAT }}
+    steps:
+    - name: Checkout Actions Repository
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Run Reports
+      id: run-reports
+      uses: ottrproject/ottr-reports@main
+      with:
+        check_spelling: ${{needs.yaml-check.outputs.toggle_spell_check}}
+        spelling_error_min: ${{needs.yaml-check.outputs.spell_error_min}}
+        check_urls: ${{needs.yaml-check.outputs.toggle_url_check}}
+        url_error_min: ${{needs.yaml-check.outputs.url_error_min}}
+        check_quiz_form: ${{needs.yaml-check.outputs.toggle_quiz_check}}
+        quiz_error_min: ${{needs.yaml-check.outputs.quiz_error_min}}
+        sort_dictionary: ${{needs.yaml-check.outputs.toggle_dictionary_sort}}
 
 ############################# Style the code ###################################
   style-code:
     name: Style code
     needs: yaml-check
     runs-on: ubuntu-latest
-    if: ${{needs.yaml-check.outputs.toggle_style_code == 'yes'}}
+    if: ${{needs.yaml-check.outputs.toggle_style_code == 'true'}}
     container:
       image: jhudsl/base_ottr:main
 
@@ -121,7 +115,7 @@ jobs:
     name: Readability report
     needs: yaml-check
     runs-on: ubuntu-latest
-    if: ${{needs.yaml-check.outputs.toggle_readability == 'yes'}}
+    if: ${{needs.yaml-check.outputs.toggle_readability == 'true'}}
 
     steps:
       - name: Checkout repo
@@ -136,127 +130,23 @@ jobs:
           glob: '**/*.md'
 
 ############################# Render Preview ###################################
-
   render-preview:
     name: Render preview
     needs: yaml-check
     runs-on: ubuntu-latest
-    container:
-      image: ${{needs.yaml-check.outputs.rendering_docker_image}}
-    if: ${{needs.yaml-check.outputs.toggle_render_preview == 'yes'}}
+    if: ${{needs.yaml-check.outputs.toggle_render_preview == 'true'}}
+    permissions:
+      pull-requests: write
+      contents: write
 
     steps:
-      - name: Checkout files
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-
-      # Set up git checkout
-      - name: Set up git checkout
-        run: |
-          git config --global --add safe.directory $GITHUB_WORKSPACE
-          git config --global user.name 'github-actions[bot]'
-          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
-
-          branch_name='preview-${{ github.event.pull_request.number }}'
-          git fetch --all
-          git checkout $branch_name
-          git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories
-        shell: bash
-
-      # Run bookdown rendering
-      - name: Run bookdown render
-        id: bookdown
-        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
-        run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
-
-      # Run quarto rendering
-      - name: Render quarto version
-        id: quarto
-        if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }}
-        run: Rscript -e "quarto::quarto_render('.')"
-
-      # This checks on the steps before it and makes sure that they completed.
-      # If the renders didn't complete we don't want to commit the file changes
-      - name: Check on Rmd render steps
-        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
-        run: |
-          echo Bookdown status ${{steps.bookdown.outcome}}
-          if [${{steps.bookdown.outcome}} != 'success']; then
-            exit 1
-          fi
-
-      - name: Check on quarto render steps
-        if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }}
-        run: |
-          echo Quarto status ${{steps.quarto.outcome}}
-          if [${{steps.quarto.outcome}} != 'success']; then
-            exit 1
-          fi
-
-      - name: Website preview for download
-        run: zip website-preview.zip docs/* -r
-
-      # Commit the rendered bookdown files
-      - name: Commit rendered bookdown files to preview branch
-        id: commit
-        run: |
-          branch_name='preview-${{ github.event.pull_request.number }}'
-          git diff origin/main -- docs >/dev/null && changes=true || changes=false
-          echo "changes=$changes" >> $GITHUB_OUTPUT
-          git add . --force
-          git commit -m 'Render preview' || echo "No changes to commit"
-          git pull --rebase --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
-          git push --force || echo "No changes to commit"
-        shell: bash
-
-      - name: Find Comment
-        uses: peter-evans/find-comment@v2
-        id: fc
-        with:
-          issue-number: ${{ github.event.pull_request.number }}
-          comment-author: 'github-actions[bot]'
-          body-includes: latest commit
-
-      - name: Build components of the comment
-        id: build-components
-        run: |
-          course_name=$(head -n 1 _bookdown.yml | cut -d'"' -f 2| tr " " "-")
-          bookdown_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/index.html")
-          docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/docs/$course_name.docx")
-          zip_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/website-preview.zip")
-          echo "zip_link=$zip_link" >> $GITHUB_OUTPUT
-          echo "bookdown_link=$bookdown_link" >> $GITHUB_OUTPUT
-          echo "docx_link=$docx_link" >> $GITHUB_OUTPUT
-          echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
-          echo "commit_id=$GITHUB_SHA" >> $GITHUB_OUTPUT
-          echo ${{steps.commit.outputs.changes}}
-
-      - name: Create or update comment
-        if: steps.commit.outputs.changes == 'true'
-        uses: peter-evans/create-or-update-comment@v2
-        with:
-          comment-id: ${{ steps.fc.outputs.comment-id }}
-          issue-number: ${{ github.event.pull_request.number }}
-          body: |
-            Re-rendered previews from the latest commit:
-            - :eyes: Quick [preview of course website here](${{ steps.build-components.outputs.bookdown_link }}) \*
-            - :microscope: Comprehensive [download of the course website here](${{ steps.build-components.outputs.zip_link }})
-            - Download the [.docx file](${{ steps.build-components.outputs.docx_link }})
-
-            \* note not all html features will be properly displayed in the "quick preview" but it will give you a rough idea.
-
-            _Updated at ${{ steps.build-components.outputs.time }} with changes from the latest commit ${{ steps.build-components.outputs.commit_id }}_
-          edit-mode: replace
-
-      - name: Comment if no changes
-        if: steps.commit.outputs.changes == 'false'
-        uses: peter-evans/create-or-update-comment@v2
-        with:
-          comment-id: ${{ steps.fc.outputs.comment-id }}
-          issue-number: ${{ github.event.pull_request.number }}
-          body: |
-            The latest commit did not produce rendering changes.
-
-            _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
-          edit-mode: replace
+    - name: Checkout repo
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Run render
+      uses: ottrproject/ottr-preview@main
+      with:
+        toggle_website: ${{needs.yaml-check.outputs.toggle_website}}
+        docker_image: ${{needs.yaml-check.outputs.rendering_docker_image}}
diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 56dffb7..e404e09 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -1,5 +1,5 @@
 # Candace Savonen 2021
-# Updated May 2024
+# Updated April 2025
 
 name: Render all output courses
 
@@ -39,8 +39,6 @@ jobs:
     name: Render course preview
     needs: yaml-check
     runs-on: ubuntu-latest
-    container:
-      image: ${{needs.yaml-check.outputs.rendering_docker_image}}
 
     steps:
       - name: checkout
@@ -49,60 +47,14 @@ jobs:
           fetch-depth: 0
           token: ${{ secrets.GH_PAT }}
 
-      - name: Login as github actions bot
-        run: |
-          git config --global --add safe.directory $GITHUB_WORKSPACE
-          git config --global user.name 'github-actions[bot]'
-          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
-
-      # We want a fresh run of the renders each time
-      - name: Delete old docs/*
-        run: |
-          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
-          git fetch origin
-          git pull --rebase --allow-unrelated-histories --strategy-option=ours
-
-      # Run Rmd rendering
-      - name: Run bookdown render
-        id: bookdown
-        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
-        run: |
-          rm -rf docs/*
-          Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all');
-          file.copy(from = 'assets', to = 'docs/assets', overwrite = TRUE)"
-
-      - name: Render quarto version
-        id: quarto
-        if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }}
-        run: Rscript -e "quarto::quarto_render('.')"
-
-      # This checks on the steps before it and makes sure that they completed.
-      # If the renders didn't complete we don't want to commit the file changes
-      - name: Check on Rmd render steps
-        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
-        run: |
-          echo Bookdown status ${{steps.bookdown.outcome}}
-          if [${{steps.bookdown.outcome}} != 'success']; then
-            exit 1
-          fi
-
-      - name: Check on quarto render steps
-        if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }}
-        run: |
-          echo Quarto status ${{steps.quarto.outcome}}
-          if [${{steps.quarto.outcome}} != 'success']; then
-            exit 1
-          fi
-
-      # Commit the rendered course files
-      - name: Commit rendered course files
-        env:
-          GH_PAT: ${{ secrets.GH_PAT }}
-        run: |
-          git add --force docs/*
-          git commit -m 'Render course' || echo "No changes to commit"
-          git status docs/*
-          git push --force -u origin main  || echo "No changes to push"
+      - name: Run render
+        id: render
+        uses: ottrproject/ottr-preview@main
+        with:
+          toggle_website: ${{needs.yaml-check.outputs.toggle_website}}
+          preview: false
+          token: ${{ secrets.GH_PAT }}
+          docker_image: ${{needs.yaml-check.outputs.rendering_docker_image}}
 
   render-tocless:
     name: Render TOC-less version for Leanpub or Coursera
@@ -110,7 +62,7 @@ jobs:
     runs-on: ubuntu-latest
     container:
       image: ${{needs.yaml-check.outputs.rendering_docker_image}}
-    if: ${{needs.yaml-check.outputs.toggle_coursera == 'yes' || needs.yaml-check.outputs.toggle_leanpub == 'yes'}}
+    if: ${{needs.yaml-check.outputs.toggle_coursera == 'true' || needs.yaml-check.outputs.toggle_leanpub == 'true'}}
 
     steps:
       - name: checkout
@@ -157,8 +109,8 @@ jobs:
     needs: [yaml-check, render-tocless]
     runs-on: ubuntu-latest
     container:
-      image: jhudsl/ottrpal
-    if: ${{needs.yaml-check.outputs.toggle_leanpub == 'yes'}}
+      image: jhudsl/base_ottr:dev
+    if: ${{needs.yaml-check.outputs.toggle_leanpub == 'true'}}
 
     steps:
       - name: checkout
@@ -184,12 +136,12 @@ jobs:
           rm -rf resources/chapt_screen_images
 
           # Make new screenshots
-          curl -o make_screenshots.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/make_screenshots.R
-          chapt_urls=$(Rscript --vanilla make_screenshots.R \
-            --git_pat ${{ secrets.GH_PAT }} \
-            --repo $GITHUB_REPOSITORY \
-            --output_dir resources/chapt_screen_images)
-          rm make_screenshots.R
+          chapt_urls=$(Rscript -e " \
+           Sys.setenv(CHROMOTE_CHROME = '/usr/bin/vivaldi'); \
+           ottrpal::make_screenshots( \
+            token = '${{ secrets.GH_PAT }}', \
+            repo = '$GITHUB_REPOSITORY' )" \
+            )
 
       # We want a fresh run of the renders each time
       - name: Delete manuscript/
@@ -201,34 +153,31 @@ jobs:
           git commit -m 'Delete manuscript folder' || echo "No changes to commit"
           git push -u origin main || echo "No changes to push"
 
-      - name: Run ottrpal::bookdown_to_embed_leanpub
-        if: ${{ needs.yaml-check.outputs.toggle_quiz_check == 'no'}}
+      - name: Run ottrpal::bookdown_to_embed_leanpub -- No Quiz
+        if: ${{ needs.yaml-check.outputs.toggle_quiz_check != 'true'}}
         run: |
-          echo needs.yaml-check.outputs.toggle_make_book_txt == 'yes'
-          echo needs.yaml-check.outputs.toggle_make_book_txt
-          Rscript -e "ottrpal::bookdown_to_embed_leanpub(
+          Rscript -e "ottrpal::website_to_embed_leanpub(
             render = FALSE, \
             chapt_img_key = 'resources/chapt_screen_images/chapter_urls.tsv', \
-            make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt == 'yes'}}'), \
+            make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt == 'true'}}'), \
             quiz_dir = NULL)"
 
-      - name: Run ottrpal::bookdown_to_embed_leanpub
-        if: ${{ needs.yaml-check.outputs.toggle_quiz_check == 'yes'}}
+      - name: Run ottrpal::bookdown_to_embed_leanpub -- with Quiz
+        if: ${{ needs.yaml-check.outputs.toggle_quiz_check == 'true'}}
         run: |
-          Rscript -e "ottrpal::bookdown_to_embed_leanpub(
+          Rscript -e "ottrpal::website_to_embed_leanpub(
             render = FALSE, \
             chapt_img_key = 'resources/chapt_screen_images/chapter_urls.tsv', \
-            make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt == 'yes'}}'))"
+            make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt == 'true'}}'))"
 
       # Commit the rendered Leanpub files
       - name: Commit rendered Leanpub files
         env:
           GH_PAT: ${{ secrets.GH_PAT }}
         run: |
-          mkdir -p manuscript
-          git add --force manuscript/*
-          git add --force resources/*
-          git add --force docs/*
+          git add --force manuscript/* || "No files to add"
+          git add --force resources/* || "No files to add"
+          git add --force docs/* || "No files to add"
           git commit -m 'Render Leanpub' || echo "No changes to commit"
           git status docs/*
           git pull --rebase --allow-unrelated-histories --strategy-option=ours --autostash
@@ -240,7 +189,7 @@ jobs:
     runs-on: ubuntu-latest
     container:
       image: ${{needs.yaml-check.outputs.rendering_docker_image}}
-    if: ${{needs.yaml-check.outputs.toggle_coursera == 'yes'}}
+    if: ${{needs.yaml-check.outputs.toggle_coursera == 'true'}}
 
     steps:
       - name: checkout
@@ -260,7 +209,7 @@ jobs:
 
       # Run Coursera version
       - name: Convert Leanpub quizzes to Coursera
-        if: needs.yaml-check.outputs.toggle_leanpub == 'yes' && needs.yaml-check.outputs.toggle_quiz_check == 'yes'
+        if: needs.yaml-check.outputs.toggle_leanpub == 'true' && needs.yaml-check.outputs.toggle_quiz_check == 'true'
         id: coursera
         run: Rscript -e "ottrpal::convert_coursera_quizzes()"
 
@@ -273,7 +222,6 @@ jobs:
           if [ -d 'coursera_quizzes' ]; then
             git add --force coursera_quizzes/*
           fi
-          git add --force manuscript/*
           git add --force resources/*
           git add --force docs/*
           git commit -m 'Render Coursera quizzes' || echo "No changes to commit"
diff --git a/05-scientific-notebooks.Rmd b/05-scientific-notebooks.Rmd
index 66287d5..34162ce 100644
--- a/05-scientific-notebooks.Rmd
+++ b/05-scientific-notebooks.Rmd
@@ -152,7 +152,7 @@ From @Shapiro2021
 More reading about RStudio's interface:
 
 - [RStudio IDE Cheatsheet (pdf)](https://rstudio.github.io/cheatsheets/html/rstudio-ide.html).
-- [Navigating the RStudio Interface - R for Epidemiology](https://www.r4epi.com/navigating-the-rstudio-interface.html)
+- [Navigating the RStudio Interface - R for Epidemiology](https://www.r4epi.com/chapters/navigating_rstudio/navigating_rstudio)
 
 </details>
 
diff --git a/07-durable-code.Rmd b/07-durable-code.Rmd
index e8a88cb..9e79248 100644
--- a/07-durable-code.Rmd
+++ b/07-durable-code.Rmd
@@ -44,7 +44,7 @@ We'll talk a bit more about code review in an upcoming chapter!
 
 - [Readable Code](https://blog.pragmaticengineer.com/readable-code/) by @Orosz2019.    
 - [Write clean R code](https://appsilon.com/write-clean-r-code/) by @Dubel2021.  
-- [Python Clean Code: 6 Best Practices to Make Your Python Functions More Readable](https://towardsdatascience.com/python-clean-code-6-best-practices-to-make-your-python-functions-more-readable-7ea4c6171d60) by @Tran2021.  
+- [Python Clean Code: 6 Best Practices to Make Your Python Functions More Readable](https://medium.com/data-science/python-clean-code-6-best-practices-to-make-your-python-functions-more-readable-7ea4c6171d60) by @Tran2021.  
 
 #### DRY up your code
 <img src="resources/images/DRY.png" width="12%">
@@ -191,8 +191,8 @@ Try to avoid using variable names that have no meaning like `tmp` or `x`, or `i`
 
 **More reading:**  
 
-- [R for Epidemiology - Coding best Practices](https://www.r4epi.com/coding-best-practices.html#object-variable-names) by @Cannell2021.
-- [Data Scientists: Your Variable Names Are Awful. Here’s How to Fix Them](https://towardsdatascience.com/data-scientists-your-variable-names-are-awful-heres-how-to-fix-them-89053d2855be) by @Koehrsen2019.  
+- [R for Epidemiology - Coding best Practices](https://www.r4epi.com/chapters/best_practices/best_practices#object-variable-names) by @Cannell2021.
+- [Data Scientists: Your Variable Names Are Awful. Here’s How to Fix Them](https://willkoehrsen.github.io/data%20science/software%20engineering/data-scientists-your-variable-names-are-awful-heres-how-to-fix-them/) by @Koehrsen2019. 
 - [Writing Variable — Informative, Descriptive & Elegant](https://medium.datadriveninvestor.com/writing-variable-informative-descriptive-elegant-1dd6f3f15db3) by @Hobert2018.   
 
 #### Follow a code style
@@ -301,7 +301,7 @@ There's so many opinions and strategies on best practices for code. And although
 
 - [Data Carpentry's: Best Practices for Writing R Code](https://swcarpentry.github.io/r-novice-inflammation/06-best-practices-R.html) by @DataCarpentry2021b.
 - [R Programming for Research: Reproducible Research](https://geanders.github.io/RProgrammingForResearch/reproducible-research-1.html) by @Good2021.
-- [R for Epidemiology: Coding best practices](https://www.r4epi.com/coding-best-practices.html) by @Cannell2021.
+- [R for Epidemiology: Coding best practices](https://www.r4epi.com/chapters/best_practices/best_practices) by @Cannell2021.
 - [Best practices for R Programming](https://towardsdatascience.com/best-practices-for-r-programming-ec0754010b5a) by @Bernardo2021.
 
 ## Get the exercise project files (or continue with the files you used in the previous chapter)
diff --git a/08-readmes.Rmd b/08-readmes.Rmd
index 7dd0d66..8d645a5 100644
--- a/08-readmes.Rmd
+++ b/08-readmes.Rmd
@@ -67,7 +67,7 @@ You can take a look at this [template README](https://raw.githubusercontent.com/
 
 - [How to write a good README file](https://www.freecodecamp.org/news/how-to-write-a-good-readme-file/)
 - [A Beginners Guide to writing a Kicka** README](https://meakaakka.medium.com/a-beginners-guide-to-writing-a-kickass-readme-7ac01da88ab3)
-- [How to write an awesome README](https://towardsdatascience.com/how-to-write-an-awesome-readme-68bf4be91f8b)
+- [Tips for Creating Great README Docs](https://www.archbee.com/blog/readme-creating-tips)
 
 ## Get the exercise project files (or continue with the files you used in the previous chapter)
 
diff --git a/assets/style.css b/assets/style.css
new file mode 100755
index 0000000..587dd94
--- /dev/null
+++ b/assets/style.css
@@ -0,0 +1,441 @@
+/* variables are set in style_config_default.css */
+
+@import url('https://fonts.googleapis.com/css?family=Abril+Fatface|Karla:400,400i,700,700i|Lora:400,400i,700,700i&display=swap');
+
+p.caption {
+  color: var(--caption-color);
+  margin-top: 10px;
+}
+p code {
+  white-space: inherit;
+}
+pre {
+  word-break: normal;
+  word-wrap: normal;
+}
+pre code {
+  white-space: inherit;
+}
+
+/*---------------Hero Image------------------*/
+
+/* next 3 rules are for setting large image at top of each page and pushing down the book content to appear beneath the image */
+
+.hero-image-container {
+  position: absolute;
+  top: 0;
+  left: 0;
+  right: 0;
+  height: 200px;
+  /*background-image: url("images/books.jpg");*/
+  /*background-color: #193a5c;*/
+}
+
+.hero-image {
+  width: 100%;
+  height: 80%;
+  /*object-fit: cover;*/
+}
+
+.page-inner {
+  padding-top: 140px !important;
+}
+
+
+/* ------------Links------------------ */
+
+.book .book-body .page-wrapper .page-inner section.normal a {
+  color: var(--link-color);
+  text-decoration: underline;
+}
+
+
+/*------------- Body and header text---------------- */
+
+.book.font-family-1 {
+  font-family: 'Karla', arial, sans-serif;
+}
+
+h1, h2, h3, h4 {
+  font-family: 'Lora', arial, sans-serif;
+}
+
+
+.book .book-body .page-wrapper .page-inner section.normal h1,
+.book .book-body .page-wrapper .page-inner section.normal h2,
+.book .book-body .page-wrapper .page-inner section.normal h3,
+.book .book-body .page-wrapper .page-inner section.normal h4,
+.book .book-body .page-wrapper .page-inner section.normal h5,
+.book .book-body .page-wrapper .page-inner section.normal h6 {
+    margin-top: 2.275em;
+    margin-bottom: 1em;
+}
+
+.title {
+  font-family: 'Lora';
+  font-size: 4em !important;
+  color: var(--accent-color);
+  margin-top: 0.275em !important;
+  margin-bottom: 0.35em !important;
+}
+
+.subtitle {
+  font-family: 'Lora';
+  color: var(--link-color);
+}
+
+
+/*----------DROP CAPS--------------*/
+
+
+/*p:nth-child(2):first-letter {   /* /* DROP-CAP FOR FIRST P BENEATH EACH H1 OR H2*/ /*
+  color: #3fb5bd;
+  float: left;
+  font-family: 'Abril Fatface', serif;
+  font-size: 7em;
+  line-height: 65px;
+  padding-top: 4px;
+  padding-right: 8px;
+  padding-left: 3px;
+  margin-bottom: 9px;
+}
+*/
+
+.section.level1 > p:first-of-type:first-letter { /*drop cap for first p beneath level 1 headers only within class .section*/
+  color: var(--accent-color);
+  float: left;
+  font-family: 'Abril Fatface', serif;
+  font-size: 7em;
+  line-height: 65px;
+  padding-top: 4px;
+  padding-right: 8px;
+  padding-left: 3px;
+  margin-bottom: 9px;
+}
+
+/* add drop cap to first paragraph that follows the first 2nd level header*/
+/*
+.section.level2:first-of-type > p:first-of-type:first-letter {
+  color: #3fb5bd;
+  float: left;
+  font-family: 'Abril Fatface', serif;
+  font-size: 7em;
+  line-height: 65px;
+  padding-top: 4px;
+  padding-right: 8px;
+  padding-left: 3px;
+  margin-bottom: 9px;
+}
+*/
+
+
+
+/*------------ TOC --------------*/
+
+
+.book .book-summary {
+  background: var(--background-color);
+  border-right: none;
+}
+
+/*---color of links in TOC----*/
+
+.book .book-summary a {
+color: var(--accent-color)
+}
+
+.summary{
+  font-family: 'Karla', sans-serif;
+}
+
+/* all TOC list items, basically */
+.book .book-summary ul.summary li a,
+.book .book-summary ul.summary li span {
+  padding-top: 8px;
+  padding-bottom: 8px;
+  padding-left: 15px;
+  padding-right: 15px;
+  color: var(--accent-color);
+}
+
+.summary a:hover {
+  color: var(--highlight-color) !important;
+}
+
+.book .book-summary ul.summary li.active>a { /*active TOC links*/
+  color: var(--link-color) !important;
+  border-left: solid 4px;
+  border-color: var(--highlight-color);
+  padding-left: 11px !important;
+}
+
+
+li.appendix span, li.part span { /* for TOC part names */
+  margin-top: 1em;
+  color: #000000;
+  opacity: .9 !important;
+  text-transform: uppercase;
+}
+
+.part + li[data-level=""] { /* grabs first .chapter immediately after .part...but only those ch without numbers */
+ text-transform: uppercase;
+}
+
+
+/* The next two rules make the horizontal line go straight across in top navbar */
+
+.summary > li:first-child {
+	height: 50px;
+	padding-top: 10px;
+	border-bottom: 1px solid rgba(0,0,0,.07);
+}
+
+.book .book-summary ul.summary li.divider {
+	height: 0px;
+}
+
+
+/*--- LOGO ---*/
+
+.toc-logo {
+  width: 200px !important;
+  object-fit: contain;
+  margin: 0 auto;
+}
+
+.toc-logo img {
+  max-width: 100%;
+  margin-bottom: 10px;
+}
+
+.summary > li:first-child {
+  height: auto !important;
+}
+
+/* --------------Two columns--------------- */
+
+.col2 {
+  columns: 2 200px;         /* number of columns and width in pixels*/
+  -webkit-columns: 2 200px; /* chrome, safari */
+  -moz-columns: 2 200px;    /* firefox */
+}
+
+
+.side-by-side {
+  display: flex;
+}
+
+.side1 {
+  width: 40%;
+}
+
+.side2 {
+  width: 58%;
+  margin-left: 1rem;
+}
+
+/* --------------Even split- two columns--------------- */
+
+.split {
+  display: flex;
+}
+
+.split1 {
+  width: 50%;
+  padding-right: 20px;
+}
+
+.split2 {
+  width: 50%;
+}
+
+
+/* Sidebar formating --------------------------------------------*/
+/* from r-pkgs.org*/
+
+div.notice, div.warning, div.github, div.dictionary, div.reflection, div.wip {
+  padding: 1em;
+  margin: 1em 0;
+  padding-left: 100px;
+  min-height: 120px;
+  background-repeat: no-repeat;
+}
+
+div.notice{
+  border: 4px var(--highlight-color);
+  border-style: solid;
+  background-size: 70px;
+  background-position: 15px center;
+  background-color: var(--callout-background-color);
+  background-image: url("../assets/box_images/note.png");
+}
+
+
+div.warning{
+  border: 4px #e0471c;
+  border-style: solid;
+  background-size: 70px;
+  background-position: 15px center;
+  background-color: var(--callout-background-color);
+  background-image: url("../assets/box_images/warning.png");
+}
+
+div.github{
+  border: 4px #000000;
+  border-style: solid;
+  background-size: 70px;
+  background-position: 15px center;
+  background-color: var(--callout-background-color);
+  background-image: url("../assets/box_images/github.png");
+}
+
+div.dictionary{
+  border: 4px var(--highlight-color);
+  border-style: solid;
+  background-size: 70px;
+  background-position: 15px center;
+  background-color: var(--callout-background-color);
+  background-image: url("../assets/box_images/dictionary.png");
+}
+
+div.reflection{
+  border: 4px var(--highlight-color);
+  border-style: solid;
+  background-size: 90px;
+  background-position: 15px center;
+  background-color: var(--callout-background-color);
+  background-image: url("../assets/box_images/thinking_face.png");
+}
+
+div.wip{
+  border: 4px #000000;
+  border-style: solid;
+  background-size: 70px;
+  background-position: 15px center;
+  background-color: #f4d03f;
+  background-image: url("../assets/box_images/under_construction.png");
+}
+
+/* .book .book-body .page-wrapper .page-inner section.normal is needed
+   to override the styles produced by gitbook, which are ridiculously
+   overspecified. Goal of the selectors is to ensure internal "margins"
+   controlled only by padding of container */
+
+.book .book-body .page-wrapper .page-inner section.normal div.rstudio-tip > :first-child,
+.book .book-body .page-wrapper .page-inner section.normal div.tip > :first-child {
+  margin-top: 0;
+}
+
+.book .book-body .page-wrapper .page-inner section.normal div.rstudio-tip > :last-child,
+.book .book-body .page-wrapper .page-inner section.normal div.tip > :last-child {
+  margin-bottom: 0;
+}
+
+iframe {
+   -moz-transform-origin: top left;
+   -webkit-transform-origin: top left;
+   -o-transform-origin: top left;
+   -ms-transform-origin: top left;
+   transform-origin: top left;
+}
+
+.iframe-container {
+  overflow: auto;
+  -webkit-overflow-scrolling: touch;
+  border: #ddd 2px solid;
+  box-shadow: #888 0px 5px 8px;
+  margin-bottom: 1em;
+}
+
+.iframe-container > iframe {
+  border: none;
+}
+
+
+/* -------Clipboard copy button --------- */
+.copy {
+  width: inherit;
+  background-color: #e2e2e2 ;
+  border: none;
+  border-radius: 2px;
+  float: right;
+  font-size: 60%;
+  padding: 4px 4px 4px 4px;
+}
+
+/* for new copy button */
+
+.hasCopyButton {
+  position: relative;
+}
+
+.btn-copy-ex {
+  position: absolute;
+  right: 0;
+  top: 0;
+  visibility: hidden;
+}
+
+.hasCopyButton:hover button.btn-copy-ex {
+  visibility: visible;
+}
+
+
+
+/* -----------Section anchors -------------*/
+
+.book .book-body .page-wrapper .page-inner section.normal {
+  overflow: visible !important; /*so anchor link doesn't get cut off */
+}
+
+a.anchor {
+  margin-left: -30px;
+  padding-right: 3px;
+  display:inline-block;
+  width: 30px;
+  height: 30px;
+  /*visibility: hidden;*/
+  background-image: url(https://image.flaticon.com/icons/svg/34/34735.svg) !important;
+  background-repeat: no-repeat !important;
+  background-size: 20px 20px !important;
+  background-position: center bottom !important;
+  opacity: 0;
+}
+
+
+.hasAnchor:hover a.anchor,
+a.anchor:hover {
+  /*visibility: visible;*/
+  opacity: 0.6;
+}
+
+/* disable anchors for headers with "no-anchor" class */
+.no-anchor .hasAnchor:hover a.anchor,
+.no-anchor a.anchor:hover {
+  opacity: 0 !important;
+}
+
+@media (max-width: 1144px) { /* don't show anchor link on small screens */
+  .hasAnchor:hover a.anchor {
+    visibility: hidden;
+  }
+}
+
+
+/*____Code Chunks____*/
+
+.sourceCode {
+  margin-bottom: 0.85em; /* adds same amount of margin as a <p> would */
+}
+
+.sourceCode pre {
+  margin: 0 !important; /* makes space above and below symmetrical*/
+}
+
+/* Footer */
+
+.footer {
+  font-family: "Lora", serif;
+  font-size: .85em;
+  color: var(--accent-color);
+}
diff --git a/assets/style_config_default.css b/assets/style_config_default.css
new file mode 100644
index 0000000..1c7f4bd
--- /dev/null
+++ b/assets/style_config_default.css
@@ -0,0 +1,8 @@
+:root {
+    --link-color: #0b5b9d;
+    --accent-color: #012d72;   /* book title, first letter of chapter, toc text */
+    --highlight-color: #68ace5;   /* toc highlight, callout box borders */
+    --caption-color: #595959;
+    --background-color: white;
+    --callout-background-color: #e8ebee;
+  }
\ No newline at end of file
diff --git a/book.bib b/book.bib
index fd346c8..4430659 100644
--- a/book.bib
+++ b/book.bib
@@ -135,7 +135,7 @@ @website{Bryan2021
 
 @book{Cannell2021,
 	title = {9 {Coding} best practices {\textbar} {R} for {Epidemiology}},
-	url = {https://brad-cannell.github.io/r4epi/},
+	url = {https://www.r4epi.com/},
 	abstract = {This is the textbook for Brad Cannell’s Introduction to R Programming for Epidemiologic Research course.},
 	urldate = {2021-11-02},
 	author = {Cannell, Brad},
@@ -548,7 +548,7 @@ @misc{Kostyuk2020
 @misc{Koehrsen2019,
 	title = {Data {Scientists}: {Your} {Variable} {Names} {Are} {Awful}. {Here}’s {How} to {Fix} {Them}.},
 	shorttitle = {Data {Scientists}},
-	url = {https://towardsdatascience.com/data-scientists-your-variable-names-are-awful-heres-how-to-fix-them-89053d2855be},
+	url = {https://willkoehrsen.github.io/data%20science/software%20engineering/data-scientists-your-variable-names-are-awful-heres-how-to-fix-them/},
 	abstract = {A Simple Way to Greatly Improve Code Quality},
 	language = {en},
 	urldate = {2021-10-29},
@@ -919,7 +919,7 @@ @misc{Tidyverse2021
 @misc{Tran2021,
 	title = {Python {Clean} {Code}: 6 {Best} {Practices} to {Make} your {Python} {Functions} more {Readable}},
 	shorttitle = {Python {Clean} {Code}},
-	url = {https://towardsdatascience.com/python-clean-code-6-best-practices-to-make-your-python-functions-more-readable-7ea4c6171d60},
+	url = {https://medium.com/data-science/python-clean-code-6-best-practices-to-make-your-python-functions-more-readable-7ea4c6171d60},
 	abstract = {Stop Writing Python Functions that Take more than 3 Minutes to Understand},
 	language = {en},
 	urldate = {2021-11-05},
diff --git a/config_automation.yml b/config_automation.yml
index bcbe613..3c7941e 100644
--- a/config_automation.yml
+++ b/config_automation.yml
@@ -1,33 +1,39 @@
 
+### Render preview of content with changes (Rmd's and md's are checked)
+render-preview: true
+
 ##### Checks run at pull request #####
 # Check quiz formatting
-check-quizzes: no
+check-quizzes: false
+quiz_error_min: 0
 # Check that urls in the content are not broken
-url-checker: yes
-# Render preview of content with changes (Rmd's and md's are checked)
-render-preview: yes
+url-checker: true
+url_error_min: 0
 # Spell check Rmds and quizzes
-spell-check: yes
+spell-check: true
+spell_error_min: 0
+
+#### Other options
 # Style any R code
-style-code: yes
+style-code: true
 # Would you like your markdown files to be checked for formatting
-markdown-linter: yes
+markdown-linter: true
 # Would you like a readability report on your markdowns?
-readability-report: yes
+readability-report: true
 # Test build the docker image if any docker-relevant files have been changed
-docker-test: no
+docker-test: false
 # Should URLs be tested periodically?
-url-check-periodically: yes
+url-check-periodically: true
 
 ##### Renderings run upon merge to main branch #####
 # Rendering each platform's content
 render-website: rmd
-render-leanpub: yes
-render-coursera: no
+render-leanpub: true
+render-coursera: true
 
 ## Automate the creation of Book.txt file? yes/no
 ## This is only relevant if render-leanpub is yes, otherwise it will be ignored
-make-book-txt: yes
+make-book-txt: true
 
 # What docker image should be used for rendering?
 # The default is jhudsl/base_ottr:main
diff --git a/resources/dictionary.txt b/resources/dictionary.txt
index 83c8cd2..f85a53b 100644
--- a/resources/dictionary.txt
+++ b/resources/dictionary.txt
@@ -22,6 +22,8 @@ Azacytidine
 Decitabine
 DESeq
 DESeqDataset
+else's
+functionalized
 hypomethylating
 IDH
 myeloid
@@ -62,6 +64,7 @@ llinG
 Leanpub
 Ns
 nTi
+png
 pseudorandomly
 setwd
 sp