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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-9b7d6e7a
+f5fec8ad
diff --git a/01-technical-background.html b/01-technical-background.html
@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>1&nbsp; Technical background – Biological and Biomedical Data Science (DSAN 6150)</title>
+<title>Appendix A — Technical background – Biological and Biomedical Data Science (DSAN 6150)</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -30,8 +30,7 @@
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+<link href="./references.html" rel="prev">
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 <script src="site_libs/quarto-html/popper.min.js"></script>
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@@ -360,7 +359,7 @@
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+globalThis.qwebrCellDetails = [{"id":1,"code":"lambda = 1\nx <- seq(0, 10, by = 0.1)\ny <- dexp(x, rate = lambda)\nplot(x, y, type ='l')","options":{"read-only":"false","out-height":"","context":"interactive","fig-width":7,"autorun":"false","editor-quick-suggestions":"false","fig-height":5,"editor-word-wrap":"true","warning":"true","results":"markup","output":"true","comment":"","editor-font-scale":"1","editor-max-height":"","label":"unnamed-chunk-1","dpi":72,"out-width":"700px","fig-cap":"","message":"true","classes":""}},{"id":2,"code":"alpha = 1\nbeta = 1\ny = dweibull(x, shape = alpha, scale = beta)\nplot(x, y, type = 'l')","options":{"read-only":"false","out-height":"","context":"interactive","fig-width":7,"autorun":"false","editor-quick-suggestions":"false","fig-height":5,"editor-word-wrap":"true","warning":"true","results":"markup","output":"true","comment":"","editor-font-scale":"1","editor-max-height":"","label":"unnamed-chunk-2","dpi":72,"out-width":"700px","fig-cap":"","message":"true","classes":""}}];
 
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@@ -1599,7 +1598,7 @@
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-        <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./01-technical-background.html"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Technical background</span></a></li></ol></nav>
+        <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./01-technical-background.html">Appendices</a></li><li class="breadcrumb-item"><a href="./01-technical-background.html"><span class="chapter-number">A</span>&nbsp; <span class="chapter-title">Technical background</span></a></li></ol></nav>
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       <button type="button" class="btn quarto-search-button" aria-label="Search" onclick="window.quartoOpenSearch();">
@@ -1629,17 +1628,11 @@
   <a href="./index.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Introduction</span></a>
   </div>
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- <span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Technical background</span></span></a>
-  </div>
 </li>
         <li class="sidebar-item">
   <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">1</span>&nbsp; <span class="chapter-title">Summary</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
@@ -1648,6 +1641,23 @@
  <span class="menu-text">References</span></a>
   </div>
 </li>
+        <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-1" role="navigation" aria-expanded="true">
+ <span class="menu-text">Appendices</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" role="navigation" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-1" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./01-technical-background.html" class="sidebar-item-text sidebar-link active">
+ <span class="menu-text"><span class="chapter-number">A</span>&nbsp; <span class="chapter-title">Technical background</span></span></a>
+  </div>
+</li>
+      </ul>
+  </li>
     </ul>
     </div>
 </nav>
@@ -1658,17 +1668,17 @@
     <h2 id="toc-title">Table of contents</h2>
 
   <ul>
-  <li><a href="#software" id="toc-software" class="nav-link active" data-scroll-target="#software"><span class="header-section-number">1.1</span> Software</a></li>
-  <li><a href="#probability-distributions" id="toc-probability-distributions" class="nav-link" data-scroll-target="#probability-distributions"><span class="header-section-number">1.2</span> Probability distributions</a>
+  <li><a href="#software" id="toc-software" class="nav-link active" data-scroll-target="#software"><span class="header-section-number">A.1</span> Software</a></li>
+  <li><a href="#probability-distributions" id="toc-probability-distributions" class="nav-link" data-scroll-target="#probability-distributions"><span class="header-section-number">A.2</span> Probability distributions</a>
   <ul class="collapse">
-  <li><a href="#exponential-distribution" id="toc-exponential-distribution" class="nav-link" data-scroll-target="#exponential-distribution"><span class="header-section-number">1.2.1</span> Exponential distribution</a></li>
-  <li><a href="#weibull-distribution" id="toc-weibull-distribution" class="nav-link" data-scroll-target="#weibull-distribution"><span class="header-section-number">1.2.2</span> Weibull distribution</a></li>
-  <li><a href="#gamma-distribution" id="toc-gamma-distribution" class="nav-link" data-scroll-target="#gamma-distribution"><span class="header-section-number">1.2.3</span> Gamma distribution</a></li>
-  <li><a href="#poisson-distribution" id="toc-poisson-distribution" class="nav-link" data-scroll-target="#poisson-distribution"><span class="header-section-number">1.2.4</span> Poisson distribution</a></li>
+  <li><a href="#exponential-distribution" id="toc-exponential-distribution" class="nav-link" data-scroll-target="#exponential-distribution"><span class="header-section-number">A.2.1</span> Exponential distribution</a></li>
+  <li><a href="#weibull-distribution" id="toc-weibull-distribution" class="nav-link" data-scroll-target="#weibull-distribution"><span class="header-section-number">A.2.2</span> Weibull distribution</a></li>
+  <li><a href="#gamma-distribution" id="toc-gamma-distribution" class="nav-link" data-scroll-target="#gamma-distribution"><span class="header-section-number">A.2.3</span> Gamma distribution</a></li>
+  <li><a href="#poisson-distribution" id="toc-poisson-distribution" class="nav-link" data-scroll-target="#poisson-distribution"><span class="header-section-number">A.2.4</span> Poisson distribution</a></li>
   </ul></li>
-  <li><a href="#statistical-methods" id="toc-statistical-methods" class="nav-link" data-scroll-target="#statistical-methods"><span class="header-section-number">1.3</span> Statistical methods</a>
+  <li><a href="#statistical-methods" id="toc-statistical-methods" class="nav-link" data-scroll-target="#statistical-methods"><span class="header-section-number">A.3</span> Statistical methods</a>
   <ul class="collapse">
-  <li><a href="#hypthesis-testing-and-errors" id="toc-hypthesis-testing-and-errors" class="nav-link" data-scroll-target="#hypthesis-testing-and-errors"><span class="header-section-number">1.3.1</span> Hypthesis testing and errors</a></li>
+  <li><a href="#hypthesis-testing-and-errors" id="toc-hypthesis-testing-and-errors" class="nav-link" data-scroll-target="#hypthesis-testing-and-errors"><span class="header-section-number">A.3.1</span> Hypthesis testing and errors</a></li>
   </ul></li>
   </ul>
 </nav>
@@ -1960,9 +1970,9 @@ <h2 id="toc-title">Table of contents</h2>
 }
 </script>
 
-<header id="title-block-header" class="quarto-title-block default">
+<header id="title-block-header" class="quarto-title-block default"><nav class="quarto-page-breadcrumbs quarto-title-breadcrumbs d-none d-lg-block" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./01-technical-background.html">Appendices</a></li><li class="breadcrumb-item"><a href="./01-technical-background.html"><span class="chapter-number">A</span>&nbsp; <span class="chapter-title">Technical background</span></a></li></ol></nav>
 <div class="quarto-title">
-<h1 class="title"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Technical background</span></h1>
+<h1 class="title">Appendix A — Technical background</h1>
 </div>
 
 
@@ -1980,25 +1990,25 @@ <h1 class="title"><span class="chapter-number">1</span>&nbsp; <span class="chapt
 
 
 <p>This course requires fairly involved knowledge of statistics and probability. We’ll be introducing several new concepts through the semester, but we will provide refreshers of some basic concepts as a starting point for this course.</p>
-<section id="software" class="level2" data-number="1.1">
-<h2 data-number="1.1" class="anchored" data-anchor-id="software"><span class="header-section-number">1.1</span> Software</h2>
+<section id="software" class="level2" data-number="A.1">
+<h2 data-number="A.1" class="anchored" data-anchor-id="software"><span class="header-section-number">A.1</span> Software</h2>
 <p>In this class, we will use <i class="fa-brands fa-r-project" aria-label="r-project"></i> as our primary software. We expect you to be familiar with the <code>tidyverse</code> packages, and <code>ggplot2</code> for visualization.</p>
 <p>In this class, we will make extensive use of the <code>survival</code> package, as well as various specialized packages</p>
 </section>
-<section id="probability-distributions" class="level2" data-number="1.2">
-<h2 data-number="1.2" class="anchored" data-anchor-id="probability-distributions"><span class="header-section-number">1.2</span> Probability distributions</h2>
+<section id="probability-distributions" class="level2" data-number="A.2">
+<h2 data-number="A.2" class="anchored" data-anchor-id="probability-distributions"><span class="header-section-number">A.2</span> Probability distributions</h2>
 <p>You are probably familiar with the normal (Gaussian) distribution and the binomial distribution. We’ll introduce some new distributions that will be used in the class</p>
-<section id="exponential-distribution" class="level3" data-number="1.2.1">
-<h3 data-number="1.2.1" class="anchored" data-anchor-id="exponential-distribution"><span class="header-section-number">1.2.1</span> Exponential distribution</h3>
+<section id="exponential-distribution" class="level3" data-number="A.2.1">
+<h3 data-number="A.2.1" class="anchored" data-anchor-id="exponential-distribution"><span class="header-section-number">A.2.1</span> Exponential distribution</h3>
 <p>The exponential distribution has one parameter, usually denoted by <span class="math inline">\(\lambda &gt; 0\)</span> , which is also the mean of the distribution. If <span class="math inline">\(X\sim Exp(\lambda)\)</span>, then</p>
 <p><span class="math display">\[
 P(X &gt; x) = e^{-\lambda x}\quad \text{for } x &gt; 0
 \]</span></p>
 <div id="qwebr-insertion-location-1"></div>
 <noscript>Please enable JavaScript to experience the dynamic code cell content on this page.</noscript>
 </section>
-<section id="weibull-distribution" class="level3" data-number="1.2.2">
-<h3 data-number="1.2.2" class="anchored" data-anchor-id="weibull-distribution"><span class="header-section-number">1.2.2</span> Weibull distribution</h3>
+<section id="weibull-distribution" class="level3" data-number="A.2.2">
+<h3 data-number="A.2.2" class="anchored" data-anchor-id="weibull-distribution"><span class="header-section-number">A.2.2</span> Weibull distribution</h3>
 <p>The Weibull distribution is a generalization of the Exponential distribution. It is a two-parameter distribution, with the parameters called shape (<span class="math inline">\(\alpha\)</span>) and scale ( <span class="math inline">\(\beta\)</span> ). For this distribution,</p>
 <p><span class="math display">\[
 P(X &gt; x ) = e^{-(x/\beta)^\alpha}
@@ -2007,17 +2017,17 @@ <h3 data-number="1.2.2" class="anchored" data-anchor-id="weibull-distribution"><
 <div id="qwebr-insertion-location-2"></div>
 <noscript>Please enable JavaScript to experience the dynamic code cell content on this page.</noscript>
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-<section id="gamma-distribution" class="level3" data-number="1.2.3">
-<h3 data-number="1.2.3" class="anchored" data-anchor-id="gamma-distribution"><span class="header-section-number">1.2.3</span> Gamma distribution</h3>
+<section id="gamma-distribution" class="level3" data-number="A.2.3">
+<h3 data-number="A.2.3" class="anchored" data-anchor-id="gamma-distribution"><span class="header-section-number">A.2.3</span> Gamma distribution</h3>
 </section>
-<section id="poisson-distribution" class="level3" data-number="1.2.4">
-<h3 data-number="1.2.4" class="anchored" data-anchor-id="poisson-distribution"><span class="header-section-number">1.2.4</span> Poisson distribution</h3>
+<section id="poisson-distribution" class="level3" data-number="A.2.4">
+<h3 data-number="A.2.4" class="anchored" data-anchor-id="poisson-distribution"><span class="header-section-number">A.2.4</span> Poisson distribution</h3>
 </section>
 </section>
-<section id="statistical-methods" class="level2" data-number="1.3">
-<h2 data-number="1.3" class="anchored" data-anchor-id="statistical-methods"><span class="header-section-number">1.3</span> Statistical methods</h2>
-<section id="hypthesis-testing-and-errors" class="level3" data-number="1.3.1">
-<h3 data-number="1.3.1" class="anchored" data-anchor-id="hypthesis-testing-and-errors"><span class="header-section-number">1.3.1</span> Hypthesis testing and errors</h3>
+<section id="statistical-methods" class="level2" data-number="A.3">
+<h2 data-number="A.3" class="anchored" data-anchor-id="statistical-methods"><span class="header-section-number">A.3</span> Statistical methods</h2>
+<section id="hypthesis-testing-and-errors" class="level3" data-number="A.3.1">
+<h3 data-number="A.3.1" class="anchored" data-anchor-id="hypthesis-testing-and-errors"><span class="header-section-number">A.3.1</span> Hypthesis testing and errors</h3>
 
 
 </section>
@@ -2446,14 +2456,11 @@ <h3 data-number="1.3.1" class="anchored" data-anchor-id="hypthesis-testing-and-e
 </script>
 <nav class="page-navigation">
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-      <a href="./index.html" class="pagination-link" aria-label="Introduction">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Introduction</span>
+      <a href="./references.html" class="pagination-link" aria-label="References">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">References</span>
       </a>          
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-      <a href="./summary.html" class="pagination-link" aria-label="Summary">
-        <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>
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