Some changes including new title.

rafalab · Apr 22, 2024 · 72c7ba1 · 72c7ba1
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diff --git a/_quarto.yml b/_quarto.yml
@@ -6,12 +6,12 @@ execute:
   cache: true
 
 book:
-  title: Advanced Data Science
+  title: Introduction to Data Science
   subtitle: Statistics and Prediction Algorithms Through Case Studies
   reader-mode: true
   page-footer:
     left: |
-      Advanced Data Science was written by Rafael A. Irizarry
+      Introduction to Data Science was written by Rafael A. Irizarry
     right: |
       This book was built with <a href="https://quarto.org/">Quarto</a>.
   site-url: http://rafalab.dfci.harvard.edu/dsbook-part-2

diff --git a/docs/highdim/dimension-reduction.html b/docs/highdim/dimension-reduction.html
@@ -5,7 +5,7 @@
 <meta name="generator" content="quarto-1.3.353">
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 <meta name="author" content="Rafael A. Irizarry">
-<title>Advanced Data Science - 22&nbsp; Dimension reduction</title>
+<title>Introduction to Data Science - 22&nbsp; Dimension reduction</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -109,7 +109,7 @@
 <!-- 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="../">Advanced Data Science</a> 
+      <a href="../">Introduction to Data Science</a> 
         <div class="sidebar-tools-main">
     <a href="https://github.com/rafalab/dsbook-part-2" title="Source Code" class="quarto-navigation-tool px-1" aria-label="Source Code"><i class="bi bi-github"></i></a>
   <a href="" class="quarto-reader-toggle quarto-navigation-tool px-1" onclick="window.quartoToggleReader(); return false;" title="Toggle reader mode">
@@ -748,7 +748,7 @@ <h1 class="title">
 <span><span class="fu"><a href="https://rdrr.io/r/graphics/hist.html">hist</a></span><span class="op">(</span><span class="va">z</span><span class="op">[</span>,<span class="fl">1</span><span class="op">]</span>, breaks <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html">seq</a></span><span class="op">(</span><span class="op">-</span><span class="fl">4</span>,<span class="fl">4</span>,<span class="fl">0.5</span><span class="op">)</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <p>We can visualize these to see how the first component summarizes the data. In the plot below, red represents high values and blue negative values:</p>
-<div class="cell" data-layout-align="center" height="5" data-hash="dimension-reduction_cache/html/illustrate-pca-twin-heights_f45b9d5d17ca2b561c3de6d50b0cddfd">
+<div class="cell" data-layout-align="center" height="5" data-hash="dimension-reduction_cache/html/illustrate-pca-twin-heights_f66700fe465dd08f100048303c90bfdd">
 <div class="cell-output-display">
 <div class="quarto-figure quarto-figure-center">
 <figure class="figure"><p><img src="dimension-reduction_files/figure-html/illustrate-pca-twin-heights-1.png" class="img-fluid figure-img" style="width:70.0%"></p>
@@ -1213,7 +1213,7 @@ <h1 class="title">
 </nav>
 </div> <!-- /content -->
 <footer class="footer"><div class="nav-footer">
-    <div class="nav-footer-left">Advanced Data Science was written by Rafael A. Irizarry</div>   
+    <div class="nav-footer-left">Introduction to Data Science was written by Rafael A. Irizarry</div>   
     <div class="nav-footer-center">
       &nbsp;
     </div>

diff --git a/...highdim/dimension-reduction_files/figure-html/illustrate-pca-twin-heights-1.png b/...highdim/dimension-reduction_files/figure-html/illustrate-pca-twin-heights-1.png
diff --git a/docs/highdim/intro-highdim.html b/docs/highdim/intro-highdim.html
@@ -8,7 +8,7 @@
 
 <meta name="author" content="Rafael A. Irizarry">
 
-<title>Advanced Data Science - High dimensional data</title>
+<title>Introduction to Data Science - High dimensional data</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -91,7 +91,7 @@
   <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="../">Advanced Data Science</a> 
+      <a href="../">Introduction to Data Science</a> 
         <div class="sidebar-tools-main">
     <a href="https://github.com/rafalab/dsbook-part-2" title="Source Code" class="quarto-navigation-tool px-1" aria-label="Source Code"><i class="bi bi-github"></i></a>
   <a href="" class="quarto-reader-toggle quarto-navigation-tool px-1" onclick="window.quartoToggleReader(); return false;" title="Toggle reader mode">
@@ -662,7 +662,7 @@ <h1 class="title">High dimensional data</h1>
 </div> <!-- /content -->
 <footer class="footer">
   <div class="nav-footer">
-    <div class="nav-footer-left">Advanced Data Science was written by Rafael A. Irizarry</div>   
+    <div class="nav-footer-left">Introduction to Data Science was written by Rafael A. Irizarry</div>   
     <div class="nav-footer-center">
       &nbsp;
     <div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/rafalab/dsbook-part-2/blob/main/highdim/intro-highdim.qmd" class="toc-action">View source</a></p><p><a href="https://github.com/rafalab/dsbook-part-2/issues/new" class="toc-action">Report an issue</a></p></div></div></div>

diff --git a/docs/highdim/linear-algebra.html b/docs/highdim/linear-algebra.html
@@ -5,7 +5,7 @@
 <meta name="generator" content="quarto-1.3.353">
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 <meta name="author" content="Rafael A. Irizarry">
-<title>Advanced Data Science - 21&nbsp; Applied Linear Algebra</title>
+<title>Introduction to Data Science - 21&nbsp; Applied Linear Algebra</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -109,7 +109,7 @@
 <!-- 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="../">Advanced Data Science</a> 
+      <a href="../">Introduction to Data Science</a> 
         <div class="sidebar-tools-main">
     <a href="https://github.com/rafalab/dsbook-part-2" title="Source Code" class="quarto-navigation-tool px-1" aria-label="Source Code"><i class="bi bi-github"></i></a>
   <a href="" class="quarto-reader-toggle quarto-navigation-tool px-1" onclick="window.quartoToggleReader(); return false;" title="Toggle reader mode">
@@ -958,7 +958,7 @@ <h1 class="title"><span id="sec-matrix-algebra" class="quarto-section-identifier
 </nav>
 </div> <!-- /content -->
 <footer class="footer"><div class="nav-footer">
-    <div class="nav-footer-left">Advanced Data Science was written by Rafael A. Irizarry</div>   
+    <div class="nav-footer-left">Introduction to Data Science was written by Rafael A. Irizarry</div>   
     <div class="nav-footer-center">
       &nbsp;
     </div>

diff --git a/docs/highdim/matrices-in-R.html b/docs/highdim/matrices-in-R.html
@@ -5,7 +5,7 @@
 <meta name="generator" content="quarto-1.3.353">
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 <meta name="author" content="Rafael A. Irizarry">
-<title>Advanced Data Science - 20&nbsp; Matrices in R</title>
+<title>Introduction to Data Science - 20&nbsp; Matrices in R</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -109,7 +109,7 @@
 <!-- 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="../">Advanced Data Science</a> 
+      <a href="../">Introduction to Data Science</a> 
         <div class="sidebar-tools-main">
     <a href="https://github.com/rafalab/dsbook-part-2" title="Source Code" class="quarto-navigation-tool px-1" aria-label="Source Code"><i class="bi bi-github"></i></a>
   <a href="" class="quarto-reader-toggle quarto-navigation-tool px-1" onclick="window.quartoToggleReader(); return false;" title="Toggle reader mode">
@@ -1166,7 +1166,7 @@ <h1 class="title">
 </nav>
 </div> <!-- /content -->
 <footer class="footer"><div class="nav-footer">
-    <div class="nav-footer-left">Advanced Data Science was written by Rafael A. Irizarry</div>   
+    <div class="nav-footer-left">Introduction to Data Science was written by Rafael A. Irizarry</div>   
     <div class="nav-footer-center">
       &nbsp;
     </div>

diff --git a/docs/highdim/matrix-factorization.html b/docs/highdim/matrix-factorization.html
@@ -5,7 +5,7 @@
 <meta name="generator" content="quarto-1.3.353">
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 <meta name="author" content="Rafael A. Irizarry">
-<title>Advanced Data Science - 24&nbsp; Matrix Factorization</title>
+<title>Introduction to Data Science - 24&nbsp; Matrix Factorization</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -109,7 +109,7 @@
 <!-- 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="../">Advanced Data Science</a> 
+      <a href="../">Introduction to Data Science</a> 
         <div class="sidebar-tools-main">
     <a href="https://github.com/rafalab/dsbook-part-2" title="Source Code" class="quarto-navigation-tool px-1" aria-label="Source Code"><i class="bi bi-github"></i></a>
   <a href="" class="quarto-reader-toggle quarto-navigation-tool px-1" onclick="window.quartoToggleReader(); return false;" title="Toggle reader mode">
@@ -652,7 +652,7 @@ <h1 class="title">
 <div class="cell" data-layout-align="center" data-hash="matrix-factorization_cache/html/unnamed-chunk-15_51dcda555208594fd5d18b0725d9acbe">
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="http://factominer.free.fr/missMDA/index.html">missMDA</a></span><span class="op">)</span></span>
 <span><span class="va">ind</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/colSums.html">colSums</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span><span class="op">(</span><span class="va">y</span><span class="op">)</span><span class="op">)</span> <span class="op">&gt;=</span> <span class="fl">25</span> <span class="op">|</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html">colnames</a></span><span class="op">(</span><span class="va">y</span><span class="op">)</span> <span class="op">==</span> <span class="st">"3252"</span></span>
-<span><span class="va">imputed</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/missMDA/man/imputePCA.html">imputePCA</a></span><span class="op">(</span><span class="va">r</span><span class="op">[</span>,<span class="va">ind</span><span class="op">]</span>, ncp <span class="op">=</span> <span class="fl">2</span>, coeff.ridge <span class="op">=</span> <span class="va">lambda</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span><span class="va">imputed</span> <span class="op">&lt;-</span> <span class="fu">imputePCA</span><span class="op">(</span><span class="va">r</span><span class="op">[</span>,<span class="va">ind</span><span class="op">]</span>, ncp <span class="op">=</span> <span class="fl">2</span>, coeff.ridge <span class="op">=</span> <span class="va">lambda</span><span class="op">)</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <p>To see how much we improve our previous prediction, we construct a matrix with the ratings in the test set:</p>
 <div class="cell" data-layout-align="center" data-hash="matrix-factorization_cache/html/unnamed-chunk-16_859c6077f27749e51e39ea9980cac6e1">
@@ -1120,7 +1120,7 @@ <h1 class="title">
 </nav>
 </div> <!-- /content -->
 <footer class="footer"><div class="nav-footer">
-    <div class="nav-footer-left">Advanced Data Science was written by Rafael A. Irizarry</div>   
+    <div class="nav-footer-left">Introduction to Data Science was written by Rafael A. Irizarry</div>   
     <div class="nav-footer-center">
       &nbsp;
     </div>

diff --git a/docs/highdim/regularization.html b/docs/highdim/regularization.html
@@ -5,7 +5,7 @@
 <meta name="generator" content="quarto-1.3.353">
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 <meta name="author" content="Rafael A. Irizarry">
-<title>Advanced Data Science - 23&nbsp; Regularization</title>
+<title>Introduction to Data Science - 23&nbsp; Regularization</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -110,7 +110,7 @@
 <!-- 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="../">Advanced Data Science</a> 
+      <a href="../">Introduction to Data Science</a> 
         <div class="sidebar-tools-main">
     <a href="https://github.com/rafalab/dsbook-part-2" title="Source Code" class="quarto-navigation-tool px-1" aria-label="Source Code"><i class="bi bi-github"></i></a>
   <a href="" class="quarto-reader-toggle quarto-navigation-tool px-1" onclick="window.quartoToggleReader(); return false;" title="Toggle reader mode">
@@ -1161,7 +1161,7 @@ <h1 class="title">
 </nav>
 </div> <!-- /content -->
 <footer class="footer"><div class="nav-footer">
-    <div class="nav-footer-left">Advanced Data Science was written by Rafael A. Irizarry</div>   
+    <div class="nav-footer-left">Introduction to Data Science was written by Rafael A. Irizarry</div>   
     <div class="nav-footer-center">
       &nbsp;
     </div>