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NOAA-FIMS · Feb 16, 2024 · 42f073b · 42f073b
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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
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diff --git a/content/AFSC-BSAI-AtkaMackerel.html b/content/AFSC-BSAI-AtkaMackerel.html
diff --git a/content/AFSC-GOA-pollock.html b/content/AFSC-GOA-pollock.html
diff --git a/content/NEFSC-yellowtail.html b/content/NEFSC-yellowtail.html
diff --git a/content/SWFSC-sardine.html b/content/SWFSC-sardine.html
@@ -29,8 +29,8 @@
 <script src="../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
-<link href="../content/rendering.html" rel="next">
-<link href="../content/case-study-template.html" rel="prev">
+<link href="../content/acknowledgements.html" rel="next">
+<link href="../content/AFSC-BSAI-AtkaMackerel.html" rel="prev">
 <link href="../images/favicon.ico" rel="icon">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
@@ -124,12 +124,6 @@
   <a href="../content/case-study-template.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Case study template</span></a>
   </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link active">
- <span class="menu-text">SWFSC sardine case study</span></a>
-  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -160,6 +154,12 @@
   <a href="../content/AFSC-BSAI-AtkaMackerel.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">AFSC BSAI Atka Mackerel case study</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link active">
+ <span class="menu-text">SWFSC sardine case study</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -794,13 +794,13 @@ <h2 class="anchored" data-anchor-id="add-your-pages-to-the-project">Add your pag
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../content/case-study-template.html" class="pagination-link" aria-label="Case study template">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Case study template</span>
+      <a href="../content/AFSC-BSAI-AtkaMackerel.html" class="pagination-link" aria-label="AFSC BSAI Atka Mackerel case study">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">AFSC BSAI Atka Mackerel case study</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../content/rendering.html" class="pagination-link" aria-label="Rendering">
-        <span class="nav-page-text">Rendering</span> <i class="bi bi-arrow-right-short"></i>
+      <a href="../content/acknowledgements.html" class="pagination-link" aria-label="Acknowledgements">
+        <span class="nav-page-text">Acknowledgements</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
 </nav>

diff --git a/content/acknowledgements.html b/content/acknowledgements.html
@@ -29,7 +29,7 @@
 <script src="../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
-<link href="../content/AFSC-BSAI-AtkaMackerel.html" rel="prev">
+<link href="../content/SWFSC-sardine.html" rel="prev">
 <link href="../images/favicon.ico" rel="icon">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
@@ -123,12 +123,6 @@
   <a href="../content/case-study-template.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Case study template</span></a>
   </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">SWFSC sardine case study</span></a>
-  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -159,6 +153,12 @@
   <a href="../content/AFSC-BSAI-AtkaMackerel.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">AFSC BSAI Atka Mackerel case study</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">SWFSC sardine case study</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -734,8 +734,8 @@ <h1 class="title">Acknowledgments</h1>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../content/AFSC-BSAI-AtkaMackerel.html" class="pagination-link" aria-label="AFSC BSAI Atka Mackerel case study">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">AFSC BSAI Atka Mackerel case study</span>
+      <a href="../content/SWFSC-sardine.html" class="pagination-link" aria-label="SWFSC sardine case study">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">SWFSC sardine case study</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">

diff --git a/content/case-study-template.html b/content/case-study-template.html
@@ -29,7 +29,7 @@
 <script src="../site_libs/quarto-search/fuse.min.js"></script>
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
-<link href="../content/SWFSC-sardine.html" rel="next">
+<link href="../content/rendering.html" rel="next">
 <link href="../index.html" rel="prev">
 <link href="../images/favicon.ico" rel="icon">
 <script src="../site_libs/quarto-html/quarto.js"></script>
@@ -124,12 +124,6 @@
   <a href="../content/case-study-template.html" class="sidebar-item-text sidebar-link active">
  <span class="menu-text">Case study template</span></a>
   </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">SWFSC sardine case study</span></a>
-  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -160,6 +154,12 @@
   <a href="../content/AFSC-BSAI-AtkaMackerel.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">AFSC BSAI Atka Mackerel case study</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">SWFSC sardine case study</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -226,7 +226,16 @@ <h2 class="anchored" data-anchor-id="edit-and-add-your-pages">Edit and add your
 </section>
 <section id="add-a-chunk-of-code-describing-your-setup" class="level2">
 <h2 class="anchored" data-anchor-id="add-a-chunk-of-code-describing-your-setup">Add a chunk of code describing your setup</h2>
-<p>Case study files should include: * R version * TMB version * FIMS commit * Name of your stock * Name of your region * Name of the analyst</p>
+<p>Case study files should include:</p>
+<ul>
+<li>R version</li>
+<li>TMB version</li>
+<li>FIMS commit</li>
+<li>Name of your stock</li>
+<li>Name of your region</li>
+<li>Name of the analyst</li>
+</ul>
+<p>Please ensure that the <a href="https://github.com/NOAA-FIMS/case-studies/blob/main/content/setup.qmd"><code>content/setup.qmd</code></a> file is updated if the case study requires the installation of additional R packages.</p>
 </section>
 <section id="add-a-bulleted-list-and-script-describing-simplifications-you-had-to-make" class="level2">
 <h2 class="anchored" data-anchor-id="add-a-bulleted-list-and-script-describing-simplifications-you-had-to-make">Add a bulleted list and script describing simplifications you had to make</h2>
@@ -799,8 +808,8 @@ <h2 class="anchored" data-anchor-id="add-your-pages-to-the-project">Add your pag
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="../content/SWFSC-sardine.html" class="pagination-link" aria-label="SWFSC sardine case study">
-        <span class="nav-page-text">SWFSC sardine case study</span> <i class="bi bi-arrow-right-short"></i>
+      <a href="../content/rendering.html" class="pagination-link" aria-label="Rendering">
+        <span class="nav-page-text">Rendering</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
 </nav>

diff --git a/content/publishing.html b/content/publishing.html
@@ -122,12 +122,6 @@
   <a href="../content/case-study-template.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Case study template</span></a>
   </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">SWFSC sardine case study</span></a>
-  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -158,6 +152,12 @@
   <a href="../content/AFSC-BSAI-AtkaMackerel.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">AFSC BSAI Atka Mackerel case study</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">SWFSC sardine case study</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 

diff --git a/content/rendering.html b/content/rendering.html
@@ -30,7 +30,7 @@
 <script src="../site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="../">
 <link href="../content/rmarkdown.html" rel="next">
-<link href="../content/SWFSC-sardine.html" rel="prev">
+<link href="../content/case-study-template.html" rel="prev">
 <link href="../images/favicon.ico" rel="icon">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
@@ -124,12 +124,6 @@
   <a href="../content/case-study-template.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Case study template</span></a>
   </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">SWFSC sardine case study</span></a>
-  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -160,6 +154,12 @@
   <a href="../content/AFSC-BSAI-AtkaMackerel.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">AFSC BSAI Atka Mackerel case study</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">SWFSC sardine case study</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -757,8 +757,8 @@ <h2 class="anchored" data-anchor-id="step-3.-render-within-rstudio">Step 3. Rend
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../content/SWFSC-sardine.html" class="pagination-link" aria-label="SWFSC sardine case study">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">SWFSC sardine case study</span>
+      <a href="../content/case-study-template.html" class="pagination-link" aria-label="Case study template">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Case study template</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">

diff --git a/content/rmarkdown.html b/content/rmarkdown.html
@@ -158,12 +158,6 @@
   <a href="../content/case-study-template.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Case study template</span></a>
   </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">SWFSC sardine case study</span></a>
-  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -194,6 +188,12 @@
   <a href="../content/AFSC-BSAI-AtkaMackerel.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">AFSC BSAI Atka Mackerel case study</span></a>
   </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">SWFSC sardine case study</span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container">