improve plots and CI

.Rbuildignore

@@ -7,3 +7,6 @@
 ^\.travis\.yml$
 Readme*
 .github/
+^CLAUDE\.md$
+^\.claude$
+^\.idea$

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,28 @@
+## Summary
+
+<!-- Brief description of what this PR does -->
+
+## Changes
+
+<!-- List the main changes in this PR -->
+
+-
+
+## Checklist
+
+- [ ] `devtools::test()` passes locally
+- [ ] `devtools::check()` passes with no ERRORs or WARNINGs
+- [ ] Documentation updated (if applicable)
+- [ ] Tests added/updated (if applicable)
+- [ ] Backward compatible (no breaking changes to existing behavior)
+
+## Type of Change
+
+- [ ] Bug fix (non-breaking change that fixes an issue)
+- [ ] New feature (non-breaking change that adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] Documentation update
+
+## Additional Notes
+
+<!-- Any additional context, screenshots, or information -->

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

@@ -1,40 +1,66 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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]
+    branches: [main, master, develop]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, develop]
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest, r: 'devel'}
+          - {os: ubuntu-latest, r: 'release'}
+          - {os: ubuntu-latest, r: 'oldrel-1'}
+          - {os: macos-latest, r: 'release'}
+          - {os: windows-latest, r: 'release'}
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - 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-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
       - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          args: 'c("--no-manual", "--as-cran")'
 
       - name: Show testthat output
         if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        run: |
+          find check -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@main
+        uses: actions/upload-artifact@v4
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
           path: check

.github/workflows/code-quality.yaml

@@ -0,0 +1,59 @@
+# Comprehensive code quality checks
+# Includes linting, spell checking, and documentation validation
+on:
+  push:
+    branches: [main, master, develop]
+  pull_request:
+    branches: [main, master, develop]
+
+name: code-quality
+
+permissions: read-all
+
+jobs:
+  quality-checks:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install R packages
+        run: |
+          renv::install(c("lintr", "spelling", "devtools"))
+        shell: Rscript {0}
+
+      - name: Lint R Code
+        run: |
+          lints <- lintr::lint_package()
+          if (length(lints) > 0) {
+            print(lints)
+            cat("::warning::Found", length(lints), "lint issues\n")
+          } else {
+            cat("✅ No lint issues found\n")
+          }
+        shell: Rscript {0}
+
+      - name: Check Spelling
+        run: |
+          spelling_errors <- spelling::spell_check_package()
+          if (nrow(spelling_errors) > 0) {
+            print(spelling_errors)
+            cat("::warning::Found", nrow(spelling_errors), "potential spelling errors\n")
+          } else {
+            cat("✅ No spelling errors found\n")
+          }
+        shell: Rscript {0}
+
+      - name: Quality Summary
+        run: |
+          cat("## Code Quality Summary\n", file = "quality_summary.md")
+          cat("- ✅ Lint checks completed\n", file = "quality_summary.md", append = TRUE)
+          cat("- ✅ Spell checks completed\n", file = "quality_summary.md", append = TRUE)
+          cat(readLines("quality_summary.md"), sep = "\n")
+        shell: Rscript {0}

.github/workflows/lint.yaml

@@ -0,0 +1,35 @@
+# 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, develop]
+  pull_request:
+    branches: [main, master, develop]
+
+name: lint
+
+permissions: read-all
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: false

.github/workflows/pkgdown.yaml

@@ -0,0 +1,58 @@
+# 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, develop]
+  pull_request:
+    branches: [main, master, develop]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pkgdown-${{ github.event_name != 'pull_request' && github.ref || github.run_id }}
+  cancel-in-progress: ${{ github.event_name != 'pull_request' }}
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: read
+      pages: write
+      id-token: write
+    steps:
+      - uses: actions/checkout@v5
+
+      - 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: Upload to GitHub pages
+        if: github.event_name != 'pull_request'
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: "docs"
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: actions/deploy-pages@v4

.github/workflows/release.yaml

@@ -0,0 +1,63 @@
+# Workflow for CRAN release automation
+# Triggered on GitHub releases to streamline CRAN submission process
+on:
+  release:
+    types: [published]
+
+name: CRAN-release
+
+permissions: read-all
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    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::rcmdcheck, any::devtools
+          needs: check
+
+      - name: Full CRAN check
+        run: |
+          rcmdcheck::rcmdcheck(
+            args = c("--no-manual", "--as-cran", "--run-donttest"),
+            build_args = c("--no-manual", "--compact-vignettes=gs+qpdf"),
+            error_on = "warning",
+            check_dir = "check"
+          )
+        shell: Rscript {0}
+
+      - name: Build source package
+        run: R CMD build .
+
+      - name: Upload CRAN package
+        if: success()
+        uses: actions/upload-artifact@v4
+        with:
+          name: cran-package
+          path: "*.tar.gz"
+          retention-days: 30
+
+      - name: Generate release notes
+        run: |
+          echo "## CRAN Release Package Built Successfully" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "✅ Full R CMD check passed with --as-cran" >> $GITHUB_STEP_SUMMARY
+          echo "✅ Source package built: \`$(ls *.tar.gz)\`" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "📦 **Next Steps:**" >> $GITHUB_STEP_SUMMARY
+          echo "1. Download the source package from artifacts" >> $GITHUB_STEP_SUMMARY
+          echo "2. Submit to CRAN via web form or \`devtools::release()\`" >> $GITHUB_STEP_SUMMARY
+          echo "3. Monitor CRAN checks at https://cran.r-project.org/web/checks/" >> $GITHUB_STEP_SUMMARY

.github/workflows/test-coverage.yaml

@@ -0,0 +1,60 @@
+# 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, develop]
+  pull_request:
+    branches: [main, master, develop]
+
+name: test-coverage
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: false
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package