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 @@
+source("renv/activate.R")

.github/copilot-instructions.md

@@ -0,0 +1,26 @@
+# Copilot Instructions for RME Repository
+
+## CI/CD and Workflow Debugging
+
+When investigating CI/CD failures, build errors, test failures, or workflow issues:
+
+- **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 `failed_only: true` parameter to focus on failed jobs
+- Use `return_content: true` to get the actual log content for analysis
+
+## 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`
+- `systemfonts` package requires `libfontconfig1-dev`
+- Consider using `rocker/verse` Docker image for workflows to reduce installation requirements

.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

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

.github/workflows/preview.yml

@@ -39,14 +39,12 @@ jobs:
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@HEAD
-        with:
-          needs: |
-            connect
-            website
-          extra-packages: |
-            local::.
-            any::pkgdown
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libcurl4-openssl-dev libpng-dev libfontconfig1-dev
+
+      - uses: r-lib/actions/setup-renv@v2
 
       - name: Render
         if: github.event.action != 'closed' # skip the build if the PR has been closed

.github/workflows/publish.yml

@@ -32,14 +32,12 @@ jobs:
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@HEAD
-        with:
-          needs: |
-            connect
-            website
-          extra-packages: |
-            local::.
-            any::pkgdown
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libcurl4-openssl-dev libpng-dev libfontconfig1-dev
+
+      - uses: r-lib/actions/setup-renv@v2
 
       - name: Render and Publish
         uses: quarto-dev/quarto-actions/publish@HEAD

.gitignore

@@ -27,3 +27,12 @@ rsconnect
 *.md
 
 **/*.quarto_ipynb
+
+# renv files
+renv/library/
+renv/local/
+renv/cellar/
+renv/lock/
+renv/python/
+renv/sandbox/
+renv/staging/

DESCRIPTION

@@ -56,7 +56,11 @@ 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

@@ -26,7 +26,7 @@ stroke = melt(data=stroke.wide, id.vars=c('Subject','Group'),
 
 ```{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