Built site for gh-pages

.nojekyll

@@ -1 +1 @@
-d85cf2ac
+dd0d9b9c

content/SWFSC-sardine.html

@@ -29,6 +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="../images/favicon.ico" rel="icon">
 <script src="../site_libs/quarto-html/quarto.js"></script>
 <script src="../site_libs/quarto-html/popper.min.js"></script>
@@ -74,7 +76,7 @@
       <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">Customize</li></ol></nav>
+      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../content/SWFSC-sardine.html">SWFSC sardine case study</a></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();">
@@ -118,7 +120,7 @@
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../content/SwFSC-sardine.qmd" class="sidebar-item-text sidebar-link">
+  <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>
@@ -586,6 +588,18 @@ <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">
+        <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">
+      <a href="../content/rendering.html" class="pagination-link">
+        <span class="nav-page-text">Rendering</span> <i class="bi bi-arrow-right-short"></i>
+      </a>
+  </div>
+</nav>
 </div> <!-- /content -->
 <footer class="footer">
   <div class="nav-footer">

content/acknowledgements.html

@@ -119,7 +119,7 @@
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../content/SwFSC-sardine.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">SWFSC sardine case study</span></a>
   </div>
 </li>

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.qmd" rel="next">
+<link href="../content/SWFSC-sardine.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>
@@ -120,7 +120,7 @@
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../content/SwFSC-sardine.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">SWFSC sardine case study</span></a>
   </div>
 </li>
@@ -595,7 +595,7 @@ <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.qmd" class="pagination-link">
+      <a href="../content/SWFSC-sardine.html" class="pagination-link">
         <span class="nav-page-text">SWFSC sardine case study</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>

content/publishing.html

@@ -118,7 +118,7 @@
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../content/SwFSC-sardine.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">SWFSC sardine case study</span></a>
   </div>
 </li>

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.qmd" 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>
@@ -120,7 +120,7 @@
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../content/SwFSC-sardine.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">SWFSC sardine case study</span></a>
   </div>
 </li>
@@ -553,7 +553,7 @@ <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.qmd" class="pagination-link">
+      <a href="../content/SWFSC-sardine.html" class="pagination-link">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">SWFSC sardine case study</span>
       </a>          
   </div>

content/rmarkdown.html

@@ -154,7 +154,7 @@
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../content/SwFSC-sardine.qmd" class="sidebar-item-text sidebar-link">
+  <a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">SWFSC sardine case study</span></a>
   </div>
 </li>

index.html

@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>NOAA FIMS case studies - NOAA quarto simple with R</title>
+<title>NOAA FIMS case studies - Fisheries Integrated Modeling System case studies</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -20,6 +20,40 @@
   margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */ 
   vertical-align: middle;
 }
+/* CSS for syntax highlighting */
+pre > code.sourceCode { white-space: pre; position: relative; }
+pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
+pre > code.sourceCode > span:empty { height: 1.2em; }
+.sourceCode { overflow: visible; }
+code.sourceCode > span { color: inherit; text-decoration: inherit; }
+div.sourceCode { margin: 1em 0; }
+pre.sourceCode { margin: 0; }
+@media screen {
+div.sourceCode { overflow: auto; }
+}
+@media print {
+pre > code.sourceCode { white-space: pre-wrap; }
+pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
+}
+pre.numberSource code
+  { counter-reset: source-line 0; }
+pre.numberSource code > span
+  { position: relative; left: -4em; counter-increment: source-line; }
+pre.numberSource code > span > a:first-child::before
+  { content: counter(source-line);
+    position: relative; left: -1em; text-align: right; vertical-align: baseline;
+    border: none; display: inline-block;
+    -webkit-touch-callout: none; -webkit-user-select: none;
+    -khtml-user-select: none; -moz-user-select: none;
+    -ms-user-select: none; user-select: none;
+    padding: 0 4px; width: 4em;
+  }
+pre.numberSource { margin-left: 3em;  padding-left: 4px; }
+div.sourceCode
+  {   }
+@media screen {
+pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
+}
 </style>
 
 
@@ -119,7 +153,7 @@
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./content/SwFSC-sardine.qmd" class="sidebar-item-text sidebar-link">
+  <a href="./content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">SWFSC sardine case study</span></a>
   </div>
 </li>
@@ -152,22 +186,16 @@
 </nav>
 <div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
 <!-- margin-sidebar -->
-    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
-        <nav id="TOC" role="doc-toc" class="toc-active">
-    <h2 id="toc-title">On this page</h2>
-
-  <ul>
-  <li><a href="#github-set-up" id="toc-github-set-up" class="nav-link active" data-scroll-target="#github-set-up">GitHub Set-up</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/NOAA-FIMS/case-studies/edit/main/index.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/NOAA-FIMS/case-studies/blob/main/index.qmd" class="toc-action">View source</a></p><p><a href="https://github.com/NOAA-FIMS/case-studies/issues/new" class="toc-action">Report an issue</a></p></div></div></nav>
+    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar zindex-bottom">
+
     </div>
 <!-- main -->
-<main class="content column-body" id="quarto-document-content">
+<main class="content column-page-right" id="quarto-document-content">
 
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
-<h1 class="title">NOAA quarto simple with R</h1>
-<p class="subtitle lead">A simple Quarto webpage with a book layout</p>
+<h1 class="title">Fisheries Integrated Modeling System case studies</h1>
+<p class="subtitle lead">Test cases, based on regional assessments, to illustrate use of FIMS</p>
 </div>
 
 
@@ -182,19 +210,13 @@ <h1 class="title">NOAA quarto simple with R</h1>
 
 </header>
 
-<p>This is a template for a simple Quarto website that looks like a “book”. This is a common format for documentation. It includes a GitHub Action that will build the website automatically when you make changes to the files. The NOAA palette and fonts has been added to <code>theme.scss</code>. The webpage will be on the <code>gh-pages</code> branch. Serving the website files from this branch is a common way to keep all the website files from cluttering your main branch.</p>
-<p>The GitHub Action installs R so you can have R code in your qmd or Rmd files. Note, you do not need to make changes to your Rmd files unless your need Quarto features like cross-references.</p>
-<section id="github-set-up" class="level2">
-<h2 class="anchored" data-anchor-id="github-set-up">GitHub Set-up</h2>
-<ul>
-<li><p>Click the green “use template” button to make a repository with this content. Make sure to make your repo public (since GitHub Pages doesn’t work on private repos unless you have a paid account) and check box to include all the branches (so that you get the gh-pages branch). <img width="637" alt="image" src="https://user-images.githubusercontent.com/2545978/197051535-c43c62de-17e8-40bf-a536-3eea8db250c4.png"></p></li>
-<li><p>Turn on GitHub Pages under Settings &gt; Pages . You will set pages to be made from the gh-pages branch and root directory. <img width="540" alt="image" src="https://user-images.githubusercontent.com/2545978/196808262-3d2262be-b9b5-4897-bba5-fc2f056dd335.png"></p></li>
-<li><p>Turn on GitHub Actions under Settings &gt; Actions &gt; General <img width="719" alt="image" src="https://user-images.githubusercontent.com/2545978/196808404-0c075fcf-db03-4516-88dd-3143b9fca475.png"></p></li>
-<li><p>Edit the repo description and Readme to add a link to the webpage. When you edit the description, you will see the link url in the url box or you can click on the Actions tab or the Settings &gt; Pages page to find the url.</p></li>
-</ul>
+<p>These case studies demonstrate use of the Fisheries Integrated Modeling System to run a few different cases of stock assessment models.</p>
+<div class="cell">
+<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="fu">c</span>(<span class="st">"dplyr"</span>,<span class="st">"tidyr"</span>,<span class="st">"ggplot2"</span>,<span class="st">"TMB"</span>,<span class="st">"TMBhelper"</span>)</span>
+<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>remotes<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">"NOAA-FIMS/FIMS"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+</div>
 
 
-</section>
 
 </main> <!-- /main -->
 <script id="quarto-html-after-body" type="application/javascript">
@@ -545,7 +567,7 @@ <h2 class="anchored" data-anchor-id="github-set-up">GitHub Set-up</h2>
   }
 });
 </script>
-<nav class="page-navigation column-body">
+<nav class="page-navigation column-page-right">
   <div class="nav-page nav-page-previous">
   </div>
   <div class="nav-page nav-page-next">
@@ -560,7 +582,7 @@ <h2 class="anchored" data-anchor-id="github-set-up">GitHub Set-up</h2>
     <div class="nav-footer-left">© CC-1.0</div>   
     <div class="nav-footer-center">
       &nbsp;
-    </div>
+    <div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/NOAA-FIMS/case-studies/edit/main/index.qmd" class="toc-action">Edit this page</a></p><p><a href="https://github.com/NOAA-FIMS/case-studies/blob/main/index.qmd" class="toc-action">View source</a></p><p><a href="https://github.com/NOAA-FIMS/case-studies/issues/new" class="toc-action">Report an issue</a></p></div></div></div>
     <div class="nav-footer-right">This page is built with <a href="https://quarto.org/">Quarto</a>.</div>
   </div>
 </footer>