Merge pull request #165 from UCD-SERG/copilot/sub-pr-163-again

Fix pkgdown workflow: correct file paths and update deprecated actions

Author: d-morrison

.github/workflows/pkgdown.yaml

@@ -17,8 +17,8 @@ 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
@@ -44,7 +44,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Configure git
         run: |
@@ -154,7 +154,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           ref: "gh-pages"
 

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)
 ```