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NOAA-FIMS · Dec 5, 2023 · 33857a2 · 33857a2
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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-46ed2475
+b00cad95
diff --git a/content/acknowledgements.html b/content/acknowledgements.html
@@ -113,7 +113,7 @@
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../content/add-content.html" class="sidebar-item-text sidebar-link">
+  <a href="../content/add-content.qmd" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Add content</span></a>
   </div>
 </li>

diff --git a/content/add-content.html → content/case-study-template.html b/content/add-content.html → content/case-study-template.html
@@ -29,8 +29,6 @@
 <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/customizing.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>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
@@ -76,7 +74,7 @@
       <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
-      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../content/add-content.html">Add content</a></li></ol></nav>
+      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item">Customize</li></ol></nav>
       <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
       </a>
       <button type="button" class="btn quarto-search-button" aria-label="" onclick="window.quartoOpenSearch();">
@@ -114,7 +112,7 @@
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../content/add-content.html" class="sidebar-item-text sidebar-link active">
+  <a href="../content/add-content.qmd" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Add content</span></a>
   </div>
 </li>
@@ -159,9 +157,17 @@ <h2 id="toc-title">On this page</h2>
 
   <ul>
   <li><a href="#edit-and-add-your-pages" id="toc-edit-and-add-your-pages" class="nav-link active" data-scroll-target="#edit-and-add-your-pages">Edit and add your pages</a></li>
-  <li><a href="#add-your-pages-the-project" id="toc-add-your-pages-the-project" class="nav-link" data-scroll-target="#add-your-pages-the-project">Add your pages the project</a></li>
+  <li><a href="#add-a-chunk-of-code-describing-your-setup" id="toc-add-a-chunk-of-code-describing-your-setup" class="nav-link" data-scroll-target="#add-a-chunk-of-code-describing-your-setup">Add a chunk of code describing your setup</a></li>
+  <li><a href="#add-a-bulleted-list-and-script-describing-simplifications-you-had-to-make" id="toc-add-a-bulleted-list-and-script-describing-simplifications-you-had-to-make" class="nav-link" data-scroll-target="#add-a-bulleted-list-and-script-describing-simplifications-you-had-to-make">Add a bulleted list and script describing simplifications you had to make</a></li>
+  <li><a href="#add-your-script-that-sets-up-and-runs-the-model" id="toc-add-your-script-that-sets-up-and-runs-the-model" class="nav-link" data-scroll-target="#add-your-script-that-sets-up-and-runs-the-model">Add your script that sets up and runs the model</a></li>
+  <li><a href="#add-your-comparison-figures" id="toc-add-your-comparison-figures" class="nav-link" data-scroll-target="#add-your-comparison-figures">Add your comparison figures</a></li>
+  <li><a href="#add-comparison-tables" id="toc-add-comparison-tables" class="nav-link" data-scroll-target="#add-comparison-tables">Add comparison tables</a></li>
+  <li><a href="#what-was-your-experience-using-fims-what-could-we-do-to-improve-usability" id="toc-what-was-your-experience-using-fims-what-could-we-do-to-improve-usability" class="nav-link" data-scroll-target="#what-was-your-experience-using-fims-what-could-we-do-to-improve-usability">What was your experience using FIMS? What could we do to improve usability?</a></li>
+  <li><a href="#list-any-issues-that-you-ran-into-or-found" id="toc-list-any-issues-that-you-ran-into-or-found" class="nav-link" data-scroll-target="#list-any-issues-that-you-ran-into-or-found">List any issues that you ran into or found</a></li>
+  <li><a href="#what-features-are-most-important-to-add-based-on-this-case-study" id="toc-what-features-are-most-important-to-add-based-on-this-case-study" class="nav-link" data-scroll-target="#what-features-are-most-important-to-add-based-on-this-case-study">What features are most important to add based on this case study?</a></li>
+  <li><a href="#add-your-pages-to-the-project" id="toc-add-your-pages-to-the-project" class="nav-link" data-scroll-target="#add-your-pages-to-the-project">Add your pages to the project</a></li>
   </ul>
-<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/nmfs-opensci/NOAA-quarto-simple/edit/main/content/add-content.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/nmfs-opensci/NOAA-quarto-simple/blob/main/content/add-content.qmd" class="toc-action">View source</a></p><p><a href="https://github.com/nmfs-opensci/NOAA-quarto-simple/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/nmfs-opensci/NOAA-quarto-simple/edit/main/content/case-study-template.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/nmfs-opensci/NOAA-quarto-simple/blob/main/content/case-study-template.qmd" class="toc-action">View source</a></p><p><a href="https://github.com/nmfs-opensci/NOAA-quarto-simple/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
@@ -185,7 +191,6 @@ <h1 class="title">Customize</h1>
 
 <section id="edit-and-add-your-pages" class="level2">
 <h2 class="anchored" data-anchor-id="edit-and-add-your-pages">Edit and add your pages</h2>
-<p>Edit the qmd or md files in the <code>content</code> folder. qmd files can include code (R, Python, Julia) and lots of Quarto markdown bells and whistles (like call-outs, cross-references, auto-citations and much more).</p>
 <p>Each page should start with</p>
 <pre><code>---
 title: your title
@@ -196,8 +201,35 @@ <h2 class="anchored" data-anchor-id="edit-and-add-your-pages">Edit and add your
 ---</code></pre>
 <p>and start the qmd file with a level header <code>#</code>, but if using the default title yaml (in the <code>---</code> fence) is a good habit since it makes it easy for Quarto convert your qmd file to other formats (like into a presentation).</p>
 </section>
-<section id="add-your-pages-the-project" class="level2">
-<h2 class="anchored" data-anchor-id="add-your-pages-the-project">Add your pages the project</h2>
+<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>
+</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>
+<p>How I simplified my assessment * Remove seasonality * etc.</p>
+</section>
+<section id="add-your-script-that-sets-up-and-runs-the-model" class="level2">
+<h2 class="anchored" data-anchor-id="add-your-script-that-sets-up-and-runs-the-model">Add your script that sets up and runs the model</h2>
+</section>
+<section id="add-your-comparison-figures" class="level2">
+<h2 class="anchored" data-anchor-id="add-your-comparison-figures">Add your comparison figures</h2>
+</section>
+<section id="add-comparison-tables" class="level2">
+<h2 class="anchored" data-anchor-id="add-comparison-tables">Add comparison tables</h2>
+</section>
+<section id="what-was-your-experience-using-fims-what-could-we-do-to-improve-usability" class="level2">
+<h2 class="anchored" data-anchor-id="what-was-your-experience-using-fims-what-could-we-do-to-improve-usability">What was your experience using FIMS? What could we do to improve usability?</h2>
+</section>
+<section id="list-any-issues-that-you-ran-into-or-found" class="level2">
+<h2 class="anchored" data-anchor-id="list-any-issues-that-you-ran-into-or-found">List any issues that you ran into or found</h2>
+<p>Please <a href="https://github.com/NOAA-FIMS/FIMS/issues/new/choose">open an issue</a> if you found something new.</p>
+</section>
+<section id="what-features-are-most-important-to-add-based-on-this-case-study" class="level2">
+<h2 class="anchored" data-anchor-id="what-features-are-most-important-to-add-based-on-this-case-study">What features are most important to add based on this case study?</h2>
+</section>
+<section id="add-your-pages-to-the-project" class="level2">
+<h2 class="anchored" data-anchor-id="add-your-pages-to-the-project">Add your pages to the project</h2>
 <ul>
 <li>Add the files to <code>_quarto.yml</code></li>
 </ul>
@@ -554,18 +586,6 @@ <h2 class="anchored" data-anchor-id="add-your-pages-the-project">Add your pages
   }
 });
 </script>
-<nav class="page-navigation">
-  <div class="nav-page nav-page-previous">
-      <a href="../index.html" class="pagination-link">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Home</span>
-      </a>          
-  </div>
-  <div class="nav-page nav-page-next">
-      <a href="../content/customizing.html" class="pagination-link">
-        <span class="nav-page-text">Customizing</span> <i class="bi bi-arrow-right-short"></i>
-      </a>
-  </div>
-</nav>
 </div> <!-- /content -->
 <footer class="footer">
   <div class="nav-footer">

diff --git a/content/code.html b/content/code.html
@@ -148,7 +148,7 @@
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../content/add-content.html" class="sidebar-item-text sidebar-link">
+  <a href="../content/add-content.qmd" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Add content</span></a>
   </div>
 </li>

diff --git a/content/customizing.html b/content/customizing.html
@@ -30,7 +30,7 @@
 <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/add-content.html" rel="prev">
+<link href="../content/add-content.qmd" 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>
@@ -114,7 +114,7 @@
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../content/add-content.html" class="sidebar-item-text sidebar-link">
+  <a href="../content/add-content.qmd" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Add content</span></a>
   </div>
 </li>
@@ -551,7 +551,7 @@ <h2 class="anchored" data-anchor-id="examples">Examples</h2>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="../content/add-content.html" class="pagination-link">
+      <a href="../content/add-content.qmd" class="pagination-link">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Add content</span>
       </a>          
   </div>

diff --git a/content/publishing.html b/content/publishing.html
@@ -112,7 +112,7 @@
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../content/add-content.html" class="sidebar-item-text sidebar-link">
+  <a href="../content/add-content.qmd" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Add content</span></a>
   </div>
 </li>

diff --git a/content/rendering.html b/content/rendering.html
@@ -114,7 +114,7 @@
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../content/add-content.html" class="sidebar-item-text sidebar-link">
+  <a href="../content/add-content.qmd" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Add content</span></a>
   </div>
 </li>

diff --git a/content/rmarkdown.html b/content/rmarkdown.html
@@ -148,7 +148,7 @@
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../content/add-content.html" class="sidebar-item-text sidebar-link">
+  <a href="../content/add-content.qmd" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Add content</span></a>
   </div>
 </li>

diff --git a/index.html b/index.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/add-content.html" rel="next">
+<link href="./content/add-content.qmd" rel="next">
 <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>
@@ -113,7 +113,7 @@
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./content/add-content.html" class="sidebar-item-text sidebar-link">
+  <a href="./content/add-content.qmd" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Add content</span></a>
   </div>
 </li>
@@ -549,7 +549,7 @@ <h2 class="anchored" data-anchor-id="github-set-up">GitHub Set-up</h2>
   <div class="nav-page nav-page-previous">
   </div>
   <div class="nav-page nav-page-next">
-      <a href="./content/add-content.html" class="pagination-link">
+      <a href="./content/add-content.qmd" class="pagination-link">
         <span class="nav-page-text">Add content</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>