Setting up the quarto book report

Gulf-IEA · Feb 6, 2024 · aa67928 · aa67928
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diff --git a/.quarto/cites/index.json b/.quarto/cites/index.json
@@ -1 +1 @@
-{"index.qmd":[],"OA.qmd":[],"Lab-report\\OA.qmd":[]}
+{"Lab-report\\OA.qmd":[],"index.qmd":[],"OA.qmd":[]}
diff --git a/.quarto/xref/40871caf b/.quarto/xref/40871caf
@@ -1 +1 @@
-{"headings":["esr-lab-reports","caribbean-esr","some-notes"],"options":{"chapters":true},"entries":[]}
+{"options":{"chapters":true},"entries":[],"headings":["esr-lab-reports","caribbean-esr","some-notes"]}
diff --git a/Caribbean-ESR.Rproj b/Caribbean-ESR.Rproj
@@ -0,0 +1,13 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
diff --git a/OA_files/figure-html/unnamed-chunk-3-1.png b/OA_files/figure-html/unnamed-chunk-3-1.png
diff --git a/Lab-report/OA.qmd → Report_book_files/OA.qmd b/Lab-report/OA.qmd → Report_book_files/OA.qmd
diff --git a/OA_files/figure-html/unnamed-chunk-4-1.png → ...A_files/figure-html/unnamed-chunk-4-1.png b/OA_files/figure-html/unnamed-chunk-4-1.png → ...A_files/figure-html/unnamed-chunk-4-1.png
diff --git a/Lab-report/OA_test.RData → Report_book_files/OA_test.RData b/Lab-report/OA_test.RData → Report_book_files/OA_test.RData
diff --git a/_book/index.html → Report_book_files/setting_up_ESR_report.html b/_book/index.html → Report_book_files/setting_up_ESR_report.html
@@ -6,10 +6,8 @@
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
-<meta name="author" content="Carissa Gervasi">
-<meta name="dcterms.date" content="2024-02-06">
 
-<title>Caribbean ESR Lab Report</title>
+<title>setting_up_ESR_report</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -25,185 +23,61 @@
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+<link href="setting_up_ESR_report_files/libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
 
 
 </head>
 
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+<body class="fullcontent">
+
+<div id="quarto-content" class="page-columns page-rows-contents page-layout-article">
 
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-        <i class="bi bi-layout-text-sidebar-reverse"></i>
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-      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./index.html">Part 1: Intro</a></li><li class="breadcrumb-item"><a href="./index.html"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">ESR Lab Reports</span></a></li></ol></nav>
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-<!-- content -->
-<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article">
-<!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
-    <div class="pt-lg-2 mt-2 text-left sidebar-header">
-    <div class="sidebar-title mb-0 py-0">
-      <a href="./">Caribbean ESR Lab Report</a> 
-    </div>
-      </div>
-        <div class="mt-2 flex-shrink-0 align-items-center">
-        <div class="sidebar-search">
-        <div id="quarto-search" class="" title="Search"></div>
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- <span class="menu-text">Part 1: Intro</span></a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true" aria-label="Toggle section">
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-  </div>
-</li>
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-        <li class="sidebar-item sidebar-item-section">
-      <div class="sidebar-item-container"> 
-            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true">
- <span class="menu-text">Part 2: Indicators</span></a>
-          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true" aria-label="Toggle section">
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-          </a> 
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-      <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
-          <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./Lab-report/OA.html" class="sidebar-item-text sidebar-link"><span class="chapter-title">Ocean acidification indicator</span></a>
-  </div>
-</li>
-      </ul>
-  </li>
-    </ul>
-    </div>
-</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">Table of contents</h2>
-
-  <ul>
-  <li><a href="#esr-lab-reports" id="toc-esr-lab-reports" class="nav-link active" data-scroll-target="#esr-lab-reports">ESR Lab Reports</a></li>
-  <li><a href="#caribbean-esr" id="toc-caribbean-esr" class="nav-link" data-scroll-target="#caribbean-esr">Caribbean ESR</a></li>
-  <li><a href="#some-notes" id="toc-some-notes" class="nav-link" data-scroll-target="#some-notes">Some notes</a></li>
-  </ul>
-</nav>
-    </div>
-<!-- main -->
 <main class="content" id="quarto-document-content">
 
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
-<h1 class="title">Caribbean ESR Lab Report</h1>
+<h1 class="title">setting_up_ESR_report</h1>
 </div>
 
 
 
 <div class="quarto-title-meta">
 
-    <div>
-    <div class="quarto-title-meta-heading">Author</div>
-    <div class="quarto-title-meta-contents">
-             <p>Carissa Gervasi </p>
-          </div>
-  </div>
 
-    <div>
-    <div class="quarto-title-meta-heading">Published</div>
-    <div class="quarto-title-meta-contents">
-      <p class="date">February 6, 2024</p>
-    </div>
-  </div>
 
 
   </div>
 
 
 </header>
 
-<section id="esr-lab-reports" class="level2">
-<h2 class="anchored" data-anchor-id="esr-lab-reports">ESR Lab Reports</h2>
-<p>ESR lab reports are quarto books that compile the R scripts for each indicator as well as any other descriptions of how the ESR will be put together.</p>
-</section>
 <section id="caribbean-esr" class="level2">
 <h2 class="anchored" data-anchor-id="caribbean-esr">Caribbean ESR</h2>
-<p>This lab report is for the Caribbean ESR that was compiled from 2023-2024. This is the first ESR for the Caribbean region. Here we can add more text about why this ESR is being compiled.</p>
+<p>This report is for the Caribbean ESR that was compiled from 2023-2024. This is the first ESR for the Caribbean region. Here we can add more text about why this ESR is being compiled.</p>
 </section>
 <section id="some-notes" class="level2">
 <h2 class="anchored" data-anchor-id="some-notes">Some notes</h2>
-<p>This lab report was created the following way:</p>
+<p>The Caribbean ESR report was created the following way:</p>
 <ol type="1">
 <li>clone the Caribbean ESR repo into my R studio</li>
-<li>create a new folder in the repo called “Lab report”</li>
-<li>create 2 files, one called “index.qmd” and abother called “_quarto.txt” within the Lab report folder</li>
+<li>create 2 files, one called “index.qmd” and another called “_quarto.txt” in the main Caribbean ESR folder</li>
 <li>rename the “_quarto.txt” file to “_quarto.yml” in file explorer to change it into the book YAML</li>
 <li>populate the YAML document</li>
-<li>Now in order to be able to render the book as both an html and pdf (or whatever other format you want) you need to make sure all the appropriate files are in the Lab report folder. I needed to move the Caribbean-ESR.Rproj file, the .git folder, and the .gitignore files into the Lab report folder from the main Caribbean-ESR folder.</li>
+<li>Now in order to be able to render the book as both an html and pdf (or whatever other format you want) you need to make sure all the appropriate files are in the main folder. You can’t put them in sub-fold</li>
 </ol>
-
-
 </section>
 
-</main> <!-- /main -->
+</main>
+<!-- /main column -->
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 window.document.addEventListener("DOMContentLoaded", function (event) {
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@@ -437,15 +311,6 @@ <h2 class="anchored" data-anchor-id="some-notes">Some notes</h2>
   }
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-  <div class="nav-page nav-page-previous">
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-  <div class="nav-page nav-page-next">
-      <a href="./Lab-report/OA.html" class="pagination-link">
-        <span class="nav-page-text"><span class="chapter-title">Ocean acidification indicator</span></span> <i class="bi bi-arrow-right-short"></i>
-      </a>
-  </div>
-</nav>
 </div> <!-- /content -->
 
 

diff --git a/Report_book_files/setting_up_ESR_report.qmd b/Report_book_files/setting_up_ESR_report.qmd
@@ -0,0 +1,19 @@
+---
+title: "setting_up_ESR_report"
+format: html
+editor: visual
+---
+
+## Caribbean ESR
+
+This report is for the Caribbean ESR that was compiled from 2023-2024. This is the first ESR for the Caribbean region. Here we can add more text about why this ESR is being compiled.
+
+## Some notes
+
+The Caribbean ESR report was created the following way:
+
+1.  clone the Caribbean ESR repo into my R studio
+2.  create 2 files, one called "index.qmd" and another called "\_quarto.txt" in the main Caribbean ESR folder
+3.  rename the "\_quarto.txt" file to "\_quarto.yml" in file explorer to change it into the book YAML
+4.  populate the YAML document
+5.  Now in order to be able to render the book as both an html and pdf (or whatever other format you want) you need to make sure all the appropriate files are in the main folder. You can't put them in sub-fold
diff --git a/...k/site_libs/bootstrap/bootstrap-icons.css → ..._files/libs/bootstrap/bootstrap-icons.css b/...k/site_libs/bootstrap/bootstrap-icons.css → ..._files/libs/bootstrap/bootstrap-icons.css
diff --git a/.../site_libs/bootstrap/bootstrap-icons.woff → ...files/libs/bootstrap/bootstrap-icons.woff b/.../site_libs/bootstrap/bootstrap-icons.woff → ...files/libs/bootstrap/bootstrap-icons.woff
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diff --git a/_book/site_libs/bootstrap/bootstrap.min.js → ...ort_files/libs/bootstrap/bootstrap.min.js b/_book/site_libs/bootstrap/bootstrap.min.js → ...ort_files/libs/bootstrap/bootstrap.min.js