Deploying to gh-pages from @ 6b23c1a 🚀

index.html

@@ -187,7 +187,13 @@
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   <div class="sidebar-item-container"> 
   <a href="./summary.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Summary</span></span></a>
+ <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">What is Open Source?</span></span></a>
+  </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./why.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">What is the ‘why’ for using open source solutions in pharma clinical data analytics?</span></span></a>
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intro.html

@@ -153,7 +153,13 @@
         <li class="sidebar-item">
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   <a href="./summary.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Summary</span></span></a>
+ <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">What is Open Source?</span></span></a>
+  </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./why.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">What is the ‘why’ for using open source solutions in pharma clinical data analytics?</span></span></a>
   </div>
 </li>
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   </div>
   <div class="nav-page nav-page-next">
       <a href="./summary.html" class="pagination-link">
-        <span class="nav-page-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Summary</span></span> <i class="bi bi-arrow-right-short"></i>
+        <span class="nav-page-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">What is Open Source?</span></span> <i class="bi bi-arrow-right-short"></i>
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references.html

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 <script src="site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="./">
-<link href="./summary.html" rel="prev">
+<link href="./why.html" rel="prev">
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 <script src="site_libs/quarto-html/popper.min.js"></script>
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   <a href="./summary.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Summary</span></span></a>
+ <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">What is Open Source?</span></span></a>
+  </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./why.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">What is the ‘why’ for using open source solutions in pharma clinical data analytics?</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
@@ -450,8 +456,8 @@ <h1 class="title">References</h1>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="./summary.html" class="pagination-link">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Summary</span></span>
+      <a href="./why.html" class="pagination-link">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">What is the ‘why’ for using open source solutions in pharma clinical data analytics?</span></span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">

search.json

@@ -14,10 +14,38 @@
     "text": "1.1 Purpose and Background\nThere are many questions around understanding and using open source for clinical data analysis. We want to create a comprehesive knowledge base about the “state of the union” and provide an overview and ideally also answers for core questions. We need and collect input from our community to compile the knowledge base, so please join the discussions to allow a broad and complete picutre.\nIf you like to know more, please join the R/Pharma talk “The State of Open Source Technology in Clinical Data Analysis, Reporting, and Submissions”. The recording is here: 2023 R/Pharma presentation."
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+    "objectID": "summary.html#contribute",
+    "href": "summary.html#contribute",
+    "title": "2  What is Open Source?",
+    "section": "2.1 Contribute",
+    "text": "2.1 Contribute\nContribute to the discussion here:\nWhat is open source?"
+  },
+  {
+    "objectID": "summary.html#guidance",
+    "href": "summary.html#guidance",
+    "title": "2  What is Open Source?",
+    "section": "2.2 Guidance",
+    "text": "2.2 Guidance\n\nProvide your thoughts and perspectives\nProvide references to articles, webinars, presentations (citations, links)\nBe respectful in this community"
+  },
+  {
+    "objectID": "summary.html#examples",
+    "href": "summary.html#examples",
+    "title": "2  What is Open Source?",
+    "section": "2.3 Examples",
+    "text": "2.3 Examples\nExample 1: The Open Source Initiative provides a definition:\n\nFree distribution\nAvailable source code\nDerived works possible\n\nExample 2: Merriam-Webster defines open source as “having the source code freely available for possible modification and redistribution”."
+  },
+  {
+    "objectID": "why.html#contribute",
+    "href": "why.html#contribute",
+    "title": "3  What is the ‘why’ for using open source solutions in pharma clinical data analytics?",
+    "section": "3.1 Contribute",
+    "text": "3.1 Contribute\nContribute to the discussion here:\nWhat is they ‘why’ for open source?"
+  },
+  {
+    "objectID": "why.html#guidance",
+    "href": "why.html#guidance",
+    "title": "3  What is the ‘why’ for using open source solutions in pharma clinical data analytics?",
+    "section": "3.2 Guidance",
+    "text": "3.2 Guidance\n\nProvide your thoughts and perspectives\nProvide references to articles, webinars, presentations (citations, links)\nBe respectful in this community"
   }
 ]

summary.html

@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>Open Source Technology in Clinical Data Analysis - 2&nbsp; Summary</title>
+<title>Open Source Technology in Clinical Data Analysis - 2&nbsp; What is Open Source?</title>
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@@ -64,7 +30,7 @@
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 <script src="site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="./">
-<link href="./references.html" rel="next">
+<link href="./why.html" rel="next">
 <link href="./intro.html" rel="prev">
 <script src="site_libs/quarto-html/quarto.js"></script>
 <script src="site_libs/quarto-html/popper.min.js"></script>
@@ -108,7 +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="./summary.html"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Summary</span></a></li></ol></nav>
+      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./summary.html"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">What is Open Source?</span></a></li></ol></nav>
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- <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Summary</span></span></a>
+ <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">What is Open Source?</span></span></a>
+  </div>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./why.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">What is the ‘why’ for using open source solutions in pharma clinical data analytics?</span></span></a>
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 </li>
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@@ -202,14 +174,22 @@
 <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="#contribute" id="toc-contribute" class="nav-link active" data-scroll-target="#contribute"><span class="header-section-number">2.1</span> Contribute</a></li>
+  <li><a href="#guidance" id="toc-guidance" class="nav-link" data-scroll-target="#guidance"><span class="header-section-number">2.2</span> Guidance</a></li>
+  <li><a href="#examples" id="toc-examples" class="nav-link" data-scroll-target="#examples"><span class="header-section-number">2.3</span> Examples</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"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Summary</span></h1>
+<h1 class="title"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">What is Open Source?</span></h1>
 </div>
 
 
@@ -224,15 +204,39 @@ <h1 class="title"><span class="chapter-number">2</span>&nbsp; <span class="chapt
 
 </header>
 
-<p>In summary, this book has no content whatsoever.</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="dv">1</span> <span class="sc">+</span> <span class="dv">1</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
-<div class="cell-output cell-output-stdout">
-<pre><code>[1] 2</code></pre>
-</div>
-</div>
+<p>When someone says ‘open source’ - what does that mean to you?<br>
+What are the important characteristics of something that is regarded as ‘open source’?</p>
+<ul>
+<li>Does the cost matter?</li>
+<li>Does the ability to review the code matter?</li>
+<li>Does the ability to reuse the code matter?</li>
+<li>Does the ability to modify the code matter?</li>
+</ul>
+<section id="contribute" class="level2" data-number="2.1">
+<h2 data-number="2.1" class="anchored" data-anchor-id="contribute"><span class="header-section-number">2.1</span> Contribute</h2>
+<p>Contribute to the discussion here:<br>
+<a href="https://github.com/phuse-org/OSTCDA/discussions/1">What is open source?</a></p>
+</section>
+<section id="guidance" class="level2" data-number="2.2">
+<h2 data-number="2.2" class="anchored" data-anchor-id="guidance"><span class="header-section-number">2.2</span> Guidance</h2>
+<ul>
+<li><p>Provide your thoughts and perspectives</p></li>
+<li><p>Provide references to articles, webinars, presentations (citations, links)</p></li>
+<li><p>Be respectful in this community</p></li>
+</ul>
+</section>
+<section id="examples" class="level2" data-number="2.3">
+<h2 data-number="2.3" class="anchored" data-anchor-id="examples"><span class="header-section-number">2.3</span> Examples</h2>
+<p><u><strong>Example 1:</strong></u> The Open Source Initiative provides a <a href="https://opensource.org/osd/">definition</a>:</p>
+<ul>
+<li><p>Free distribution</p></li>
+<li><p>Available source code</p></li>
+<li><p>Derived works possible</p></li>
+</ul>
+<p><u><strong>Example 2:</strong></u> <a href="#0" style="font-size: 11.4pt;">Merriam-Webster</a> defines open source as “having the source code freely available for possible modification and redistribution”.</p>
 
 
+</section>
 
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   <div class="nav-page nav-page-next">
-      <a href="./references.html" class="pagination-link">
-        <span class="nav-page-text">References</span> <i class="bi bi-arrow-right-short"></i>
+      <a href="./why.html" class="pagination-link">
+        <span class="nav-page-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">What is the ‘why’ for using open source solutions in pharma clinical data analytics?</span></span> <i class="bi bi-arrow-right-short"></i>
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