Configure repository to use renv for package management

.Rbuildignore

@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^LICENSE\.md$
 ^CODE_OF_CONDUCT\.md$
 ^.*\.Rproj$

.Rprofile

@@ -0,0 +1,6 @@
+source("renv/activate.R")
+
+if (interactive()) {
+  require(usethis)
+  require(devtools)
+}

.github/copilot-instructions.md

@@ -1,8 +1,45 @@
 # GitHub Copilot Instructions
 
+> [!IMPORTANT]
+> **MANDATORY TESTING BEFORE EVERY COMMIT:**
+> 
+> Before committing ANY changes to `.qmd`, `.R`, or config files:
+> 
+> 1. **Run `quarto render` on the FULL repository** (not individual files)
+> 2. **Verify it completes successfully** (exit code 0, no errors)
+> 3. **Run linter on changed files**:
+>    - For R files: `lintr::lint("path/to/file.R")`  
+>    - For .qmd files with R code: Extract and lint R code chunks
+>    - **Fix lint issues in code you wrote or modified** - ignore pre-existing issues in unchanged code
+> 4. **Run spellcheck**: `spelling::spell_check_package()`
+>    - **Fix spelling errors you introduced** - ignore pre-existing errors
+>    - Add technical terms to `inst/WORDLIST` if needed (create file if it doesn't exist, one word per line)
+> 5. Only then commit your changes
+>
+> **CRITICAL RULES:**
+> - **CI is NOT the test** - you must test locally BEFORE pushing
+> - **NEVER rely on CI to discover rendering, lint, or spelling errors** - that's your job
+> - **ALWAYS run full `quarto render`** - testing individual files is insufficient
+> - **Only fix lint/spell issues in code YOU changed** - don't fix unrelated pre-existing issues
+> - **This is a hard requirement - no exceptions, no excuses**
+
+## General Development Principles
+
+**CRITICAL**: Do not make assumptions about what code will do - always test it yourself.
+
+- **Test your changes**: Run the actual commands to verify functionality
+- **Run `quarto render` on FULL repository**: Testing individual files misses cross-file issues
+- **Verify output**: Check that expected files are created with correct content
+- **Never claim success without evidence**: Only report that something works after you've confirmed it yourself
+
 ## Pull Request Guidelines
 
 - Always ensure that PR branch is up to date with main branch before requesting PR review
+- **ALWAYS verify all changed hyperlinks are correct before requesting PR review**:
+  - Check that internal links point to existing files/sections
+  - Verify external URLs are accessible and correct
+  - Test cross-references and anchor links
+  - Ensure relative paths are correct
 
 ## Code Formatting Guidelines
 
@@ -28,8 +65,10 @@ Example:
 When investigating CI/CD failures (build, test, or lint workflow issues):
 
 1. **Use GitHub MCP tools to inspect job logs directly**:
+   - **ALWAYS read workflow logs directly** using GitHub MCP tools (`github-mcp-server-get_job_logs`, `github-mcp-server-list_workflow_runs`)
+   - Do NOT rely on assumptions or generic troubleshooting - examine the actual error output
    - Use `list_workflow_runs` to see recent workflow runs and their status
-   - Use `get_job_logs` with `failed_only=true` to retrieve logs from failed jobs
+   - Use `get_job_logs` with `failed_only=true` and `return_content=true` to retrieve logs from failed jobs
    - These tools provide direct access to workflow run details and logs without needing to manually check GitHub UI
 
 2. **Running lintr locally**:
@@ -56,9 +95,162 @@ If the lint workflow fails with errors like "Could not find exported symbols for
 
 4. **Alternative**: Move the package from `Suggests` to `Imports` if it's truly required for the package to function
 
+## R Package Management
+
+This repository uses `renv` for reproducible R package environments:
+
+- Package versions are locked in `renv.lock`
+- All workflows use `r-lib/actions/setup-renv@v2` for dependency installation
+- CI dependencies (gh, lintr, purrr, pkgdown) are listed in DESCRIPTION Suggests
+
+## System Dependencies
+
+Some R packages require system-level libraries to compile from source:
+- `curl` package requires `libcurl4-openssl-dev`
+- `png` package requires `libpng-dev`
+- `jpeg` package requires `libjpeg-dev`
+- `systemfonts` package requires `libfontconfig1-dev`
+- Consider using `rocker/verse` Docker image for workflows to reduce installation requirements
+
 ## JAGS Dependencies
 
 This repository uses JAGS (Just Another Gibbs Sampler) for Bayesian analysis:
-- JAGS must be installed in workflows that render Quarto documents
+- JAGS must be installed in workflows that render Quarto documents (using `sudo apt-get install -y jags`)
 - R packages `rjags` and `runjags` depend on JAGS being installed
 - The lint workflow also needs these packages installed to avoid false positives
+
+## Quarto Rendering
+
+**CRITICAL REQUIREMENTS** before requesting code review:
+
+1. **Run `quarto render` yourself locally** on the full repository and ensure it passes
+2. **Verify it completes successfully** (exit code 0, no errors)
+3. **Do NOT rely solely on CI workflows** to catch rendering issues
+4. **Test the actual command and wait for completion** - do not assume success
+5. **Check exit code to confirm success** - partial output doesn't count
+6. **If quarto render fails locally**, investigate and fix the issue before pushing changes
+
+**What "successful rendering" means**:
+- The command completes without errors (exit code 0)
+- All expected output files are generated
+- No error messages in the output
+- All documents render correctly (check for missing images, broken math, etc.)
+
+**Common mistakes to avoid**:
+- Testing individual files only (use `quarto render` for full repository)
+- Not waiting for the command to complete
+- Assuming success without checking the exit code
+- Claiming "it works" without actually running the command
+- Relying on CI to catch rendering issues
+
+This ensures all dependencies are properly configured and all documents render successfully.
+
+## Linting
+
+**CRITICAL**: Always lint changed files before requesting code review and before committing.
+
+```r
+# Lint R code files you modified
+lintr::lint("path/to/modified/file.R")
+
+# Lint Quarto documents (lints R code chunks)
+lintr::lint("path/to/modified/file.qmd")
+
+# Lint all R files in the repository (use sparingly)
+lintr::lint_dir()
+```
+
+**When to lint**:
+- Before calling the `code_review` tool
+- After making changes to R files (`.R`) or Quarto documents (`.qmd`)
+- Before committing code changes
+
+**Linting workflow for changed files**:
+1. Identify which files you've changed
+2. For `.R` files: Run `lintr::lint("filename.R")` on each changed file
+3. For `.qmd` files: Run `lintr::lint("filename.qmd")` on each changed file to lint R code chunks
+4. Fix any linting errors or warnings
+5. Only then proceed to code review
+
+**Important notes**:
+- **Only fix lint issues in code you wrote or modified** - do not fix pre-existing issues in unchanged code
+- If lint errors exist in code you didn't change, ignore them - they're not your responsibility
+- The lint-changed-files workflow will flag issues, but you should catch them locally first
+
+## Spell Checking
+
+**CRITICAL**: Always run spellcheck locally BEFORE committing.
+
+```r
+# Run spell check on the entire repository
+spelling::spell_check_package()
+
+# Check specific files
+spelling::spell_check_files("README.md")
+spelling::spell_check_files("path/to/modified/file.qmd")
+```
+
+**Spell checking workflow**:
+1. Identify which files you've changed
+2. Run `spelling::spell_check_package()` to check all documentation
+3. Review any spelling errors found
+4. Either fix the spelling errors OR add legitimate technical terms to `inst/WORDLIST` (create this file if it doesn't exist, one word per line)
+5. Re-run spell check to verify all errors are resolved
+6. Only then proceed to code review or commit
+
+**Important notes**:
+- **Only fix spelling errors you introduced** - ignore pre-existing errors in unchanged files
+- Add legitimate technical terms (e.g., "renv", "Bayesian", "MCMC") to `inst/WORDLIST`
+- Don't add typos to the wordlist - fix the typos instead
+
+## Code Review Workflow
+
+**MANDATORY ORDER OF OPERATIONS** before finalizing a pull request:
+
+1. **Lint changed files FIRST**
+   - Run `lintr::lint()` on all changed `.R` and `.qmd` files
+   - Fix any linting errors or warnings
+   - See the "Linting" section above for detailed commands
+
+2. **Run spellcheck**
+   - Run `spelling::spell_check_package()`
+   - Fix spelling errors you introduced or add legitimate terms to `inst/WORDLIST`
+
+3. **Then request code review**
+   - Use the `code_review` tool to get automated feedback
+   - The tool must be called AFTER linting and spellcheck are complete
+   - Review and address any valid comments from the code review
+
+4. **Finally run security checks**
+   - Use the `codeql_checker` tool after code review
+   - Address any security vulnerabilities found
+   - Re-run if you make significant changes
+
+**CRITICAL**: Never call `code_review` without linting and spell-checking changed files first. Linting and spell-checking catch basic issues that should be fixed before more comprehensive code review.
+
+## Determining Responsibility for Workflow Failures
+
+**IMPORTANT**: Not all workflow failures are your responsibility to fix.
+
+**You ARE responsible for** fixing workflow failures if:
+- The failure is in code or files you directly modified
+- The failure is caused by changes you introduced (e.g., new dependencies, configuration changes)
+- The error message indicates an issue with YOUR specific changes
+
+**You are NOT responsible for** fixing workflow failures if:
+- The failure is in pre-existing code you didn't modify
+- Lint errors exist in unchanged files or unchanged sections of files
+- Spelling errors exist in files you didn't modify
+- The workflow itself has an environment or infrastructure issue (e.g., package installation failures, Docker issues)
+- The error occurs in lines of code that existed before your changes
+
+**How to determine responsibility**:
+1. Check the workflow logs to identify which files/lines are causing the failure
+2. Use `git diff` or `git show` to verify whether you modified those specific lines
+3. If you only modified prose (text/comments) but errors are in code blocks, those are pre-existing
+4. If the error is "file X line Y" and you didn't touch line Y, it's pre-existing
+
+**What to do**:
+- **If it's your responsibility**: Fix the issue and re-run the workflow
+- **If it's NOT your responsibility**: Document it in your PR description and notify the repository maintainer
+- **Never** fix unrelated pre-existing issues - focus on your changes only

.github/workflows/check-spelling.yaml

@@ -21,5 +21,8 @@ jobs:
         with:
           submodules: recursive
 
+      - name: Disable renv
+        run: echo "RENV_CONFIG_AUTOLOADER_ENABLED=FALSE" >> $GITHUB_ENV
+
       - name: Run Spelling Check test
         uses: insightsengineering/[email protected]

.github/workflows/lint-changed-files.yaml

@@ -17,18 +17,12 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
 
-      - name: Install JAGS
+      - name: Install system dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install -y jags
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: |
-            any::gh
-            any::lintr
-            any::purrr
-          dependencies: '"all"'
+          sudo apt-get install -y jags libcurl4-openssl-dev libpng-dev libfontconfig1-dev libjpeg-dev
+
+      - uses: r-lib/actions/setup-renv@v2
 
       - name: Add lintr options
         run: |

.github/workflows/preview.yml

@@ -39,19 +39,17 @@ jobs:
         with:
           use-public-rspm: true
 
-      - name: Install JAGS
+      - name: Install system dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install -y jags
+          sudo apt-get install -y jags libcurl4-openssl-dev libpng-dev libfontconfig1-dev libjpeg-dev
 
-      - uses: r-lib/actions/setup-r-dependencies@HEAD
-        with:
-          needs: |
-            connect
-            website
-          extra-packages: |
-            local::.
-            any::pkgdown
+      - uses: r-lib/actions/setup-renv@v2
+
+      - name: Install local package
+        run: |
+          R CMD INSTALL .
+        shell: bash
 
       - name: Render
         if: github.event.action != 'closed' # skip the build if the PR has been closed

.github/workflows/publish.yml

@@ -32,19 +32,17 @@ jobs:
         with:
           use-public-rspm: true
 
-      - name: Install JAGS
+      - name: Install system dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install -y jags
+          sudo apt-get install -y jags libcurl4-openssl-dev libpng-dev libfontconfig1-dev libjpeg-dev
 
-      - uses: r-lib/actions/setup-r-dependencies@HEAD
-        with:
-          needs: |
-            connect
-            website
-          extra-packages: |
-            local::.
-            any::pkgdown
+      - uses: r-lib/actions/setup-renv@v2
+
+      - name: Install local package
+        run: |
+          R CMD INSTALL .
+        shell: bash
 
       - name: Render and Publish
         uses: quarto-dev/quarto-actions/publish@HEAD

.gitignore

@@ -28,3 +28,12 @@ rsconnect
 !.github/copilot-instructions.md
 
 **/*.quarto_ipynb
+
+# renv files
+renv/library/
+renv/local/
+renv/cellar/
+renv/lock/
+renv/python/
+renv/sandbox/
+renv/staging/

DESCRIPTION

@@ -58,7 +58,11 @@ Suggests:
     sjPlot,
     equatiomatic,
     broom (>= 1.0.8),
-    broom.helpers (>= 1.20.0)
+    broom.helpers (>= 1.20.0),
+    gh,
+    lintr,
+    purrr,
+    pkgdown
 RoxygenNote: 7.3.3
 License: MIT + file LICENSE
 Config/build/copy-method: link

dobson-stroke-bayes-Sec-14.6.qmd

@@ -13,8 +13,8 @@
 library(dplyr)
 
 library(reshape2)
 stroke = melt(data=stroke.wide, id.vars=c('Subject','Group'), 
               value.name='ability', variable.name='week') |> 
   mutate(
     time = as.numeric(gsub('week', '', week)),
     Group = as.numeric(as.factor(Group)),
@@ -26,7 +26,7 @@
 
 ```{r}
 jags.post <- run.jags(
-  model = "inst/extdata/stroke.bugs.R",
+  model = "inst/extdata/stroke.bugs",
   data = c(
     stroke, 
     times = max(stroke$time),

inst/WORDLIST

@@ -2,7 +2,6 @@ Biostat
 Epi
 Github
 Hua
-LaTeX
 MathJax
 NoDerivatives
 NonCommercial
@@ -12,9 +11,6 @@ UC
 Zhou
 callout
 demstats
-gitmodules
 github
 qmd
-recurse
 submodule
-submodules