From e1d7822f65f2f47ab04205128ddbf19187587969 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 7 Jan 2026 07:57:54 +0000
Subject: [PATCH 1/5] Initial plan


From 8c4bec550ec6bee3ee09982a613e27ac92d72df0 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 7 Jan 2026 08:14:24 +0000
Subject: [PATCH 2/5] Fix pkgdown workflow: correct file paths and update
 deprecated actions

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
---
 .github/workflows/pkgdown.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 8eae438e..f2bb1d05 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -19,8 +19,8 @@ on:
       - 'vignettes/**'
       - '_quarto.yml'
       - '.github/workflows/pkgdown.yaml'
-      - 'Readme.md'
-      - 'Contributing.md'
+      - 'README.md'
+      - '.github/CONTRIBUTING.md'
   push:
     tags:
       - 'v[0-9]+.[0-9]+.[0-9]+'         # build on version tags
@@ -46,7 +46,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Configure git
         run: |
@@ -138,7 +138,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           ref: "gh-pages"
 

From d62b98d469887d05794a4697a73fdf889b79f13d Mon Sep 17 00:00:00 2001
From: Douglas Ezra Morrison <demorrison@ucdavis.edu>
Date: Wed, 7 Jan 2026 01:10:20 -0800
Subject: [PATCH 3/5] Update pkgdown.yaml

---
 .github/workflows/pkgdown.yaml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index f2bb1d05..b38e5c42 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -6,8 +6,6 @@
 # more info: https://github.com/rstudio/education-workflows/tree/main/examples#deploy-pkgdown-to-github-pages-with-pr-previews-and-tagged-versions
 on:
   pull_request:
-    branches:
-      - main
     types:
       - opened
       - reopened

From 969b20ae5603e7031b4ed9b05800383a4aac5e5a Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 8 Jan 2026 02:26:50 +0000
Subject: [PATCH 4/5] Fix getting-started.qmd: correct data variable references
 and remove redundant postprocess_jags_output call

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
---
 Rplots.pdf                             | Bin 0 -> 8186 bytes
 vignettes/articles/getting-started.qmd |   9 +++------
 2 files changed, 3 insertions(+), 6 deletions(-)
 create mode 100644 Rplots.pdf

diff --git a/Rplots.pdf b/Rplots.pdf
new file mode 100644
index 0000000000000000000000000000000000000000..14ab69f1b8ac1fc41e1750b9e82c5eb1b6395444
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diff --git a/vignettes/articles/getting-started.qmd b/vignettes/articles/getting-started.qmd
index 1d5621e7..75a55253 100644
--- a/vignettes/articles/getting-started.qmd
+++ b/vignettes/articles/getting-started.qmd
@@ -172,8 +172,8 @@ Plot the predicted antibody curves with credible intervals:
 #| label: plot-curves
 plot_predicted_curve(
   fitted_model,
-  id = serocalculator::ids(case_data)[1],
-  antigen_iso = case_data$antigen_iso[1]
+  ids = serocalculator::ids(simulated_data)[1],
+  antigen_iso = simulated_data$antigen_iso[1]
 )
 ```
 
@@ -183,11 +183,8 @@ Extract and summarize the posterior estimates:
 
 ```{r}
 #| label: postprocess
-# Process JAGS output
-processed_output <- postprocess_jags_output(fitted_model)
-
 # Summarize parameter estimates
-summary_stats <- post_summ(processed_output)
+summary_stats <- post_summ(fitted_model)
 print(summary_stats)
 ```
 

From e79c669923e9b86275d0be91b753a79f8d182f93 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 8 Jan 2026 02:27:49 +0000
Subject: [PATCH 5/5] Remove Rplots.pdf and add to .gitignore

Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
---
 .gitignore |   1 +
 Rplots.pdf | Bin 8186 -> 0 bytes
 2 files changed, 1 insertion(+)
 delete mode 100644 Rplots.pdf

diff --git a/.gitignore b/.gitignore
index b331e85e..f458cdc1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -27,3 +27,4 @@ docs/
 /.quarto/
 
 **/*.quarto_ipynb
+Rplots.pdf
diff --git a/Rplots.pdf b/Rplots.pdf
deleted file mode 100644
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