Adding missing figures.

Renaming cross-validation file to resampline-methods.
rafalab · Jan 4, 2024 · 057a9c4 · 057a9c4
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diff --git a/.gitignore b/.gitignore
@@ -3,7 +3,12 @@
 .RData
 .Ruserdata
 *_cache
-*_files
+highdim/*_files
+inference/*_files
+linear-models/*_files
+ml/*_files
+prob/*_files
+summaries/*_files
 .DS_Store
 copy-qmds.R
 crossref.sh

diff --git a/_quarto.yml b/_quarto.yml
@@ -71,7 +71,7 @@ book:
         - ml/evaluation-metrics.qmd
         - ml/conditionals.qmd
         - ml/smoothing.qmd
-        - ml/cross-validation.qmd
+        - ml/resampling-methods.qmd
         - ml/algorithms.qmd
         - ml/ml-in-practice.qmd
         - ml/clustering.qmd

diff --git a/docs/highdim/dimension-reduction.html b/docs/highdim/dimension-reduction.html
diff --git a/...n_files/figure-html/unnamed-chunk-7-1.png → ...s/figure-html/before-after-rotation-1.png b/...n_files/figure-html/unnamed-chunk-7-1.png → ...s/figure-html/before-after-rotation-1.png
diff --git a/docs/highdim/dimension-reduction_files/figure-html/digit-pc-boxplot-1.png b/docs/highdim/dimension-reduction_files/figure-html/digit-pc-boxplot-1.png
diff --git a/docs/highdim/dimension-reduction_files/figure-html/histograms-of-dimensions-1.png b/docs/highdim/dimension-reduction_files/figure-html/histograms-of-dimensions-1.png
diff --git a/docs/highdim/dimension-reduction_files/figure-html/rotation-diagram-1.png b/docs/highdim/dimension-reduction_files/figure-html/rotation-diagram-1.png
diff --git a/docs/highdim/intro-highdim.html b/docs/highdim/intro-highdim.html
@@ -355,7 +355,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="../ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>

diff --git a/docs/highdim/linear-algebra.html b/docs/highdim/linear-algebra.html
diff --git a/...a_files/figure-html/unnamed-chunk-7-1.png → .../figure-html/euclidean-dist-diagram-1.png b/...a_files/figure-html/unnamed-chunk-7-1.png → .../figure-html/euclidean-dist-diagram-1.png
diff --git a/docs/highdim/linear-algebra_files/figure-html/polar-coords-1.png b/docs/highdim/linear-algebra_files/figure-html/polar-coords-1.png
diff --git a/docs/highdim/matrices-in-R.html b/docs/highdim/matrices-in-R.html
@@ -373,7 +373,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="../ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>

diff --git a/docs/highdim/matrix-factorization.html b/docs/highdim/matrix-factorization.html
diff --git a/docs/highdim/matrix-factorization_files/figure-html/e-vs-pq-1.png b/docs/highdim/matrix-factorization_files/figure-html/e-vs-pq-1.png
diff --git a/docs/highdim/matrix-factorization_files/figure-html/e-vs-pq-2-1.png b/docs/highdim/matrix-factorization_files/figure-html/e-vs-pq-2-1.png
diff --git a/docs/highdim/regularization.html b/docs/highdim/regularization.html
@@ -374,7 +374,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="../ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>
@@ -599,7 +599,7 @@ <h1 class="title">
 <i class="callout-icon"></i>
 </div>
 <div class="callout-body-container">
-<p>In <a href="../ml/cross-validation.html"><span>Chapter&nbsp;29</span></a>, we provide a formal discussion of the mean squared error.</p>
+<p>In <a href="../ml/resampling-methods.html"><span>Chapter&nbsp;29</span></a>, we provide a formal discussion of the mean squared error.</p>
 </div>
 </div>
 </div>
@@ -735,7 +735,7 @@ <h1 class="title">
 </div>
 </div>
 <p>This approach will have our desired effect: when our sample size <span class="math inline">\(n_j\)</span> is very large, we obtain a stable estimate and the penalty <span class="math inline">\(\lambda\)</span> is effectively ignored since <span class="math inline">\(n_j+\lambda \approx n_j\)</span>. Yet when the <span class="math inline">\(n_j\)</span> is small, then the estimate <span class="math inline">\(\hat{\beta}_i(\lambda)\)</span> is shrunken towards 0. The larger the <span class="math inline">\(\lambda\)</span>, the more we shrink.</p>
-<p>But how do we select <span class="math inline">\(\lambda\)</span>? In <a href="../ml/cross-validation.html"><span>Chapter&nbsp;29</span></a>, we describe an approach to do this. Here we will simply compute the RMSE we for different values of <span class="math inline">\(\lambda\)</span> to illustrate the effect:</p>
+<p>But how do we select <span class="math inline">\(\lambda\)</span>? In <a href="../ml/resampling-methods.html"><span>Chapter&nbsp;29</span></a>, we describe an approach to do this. Here we will simply compute the RMSE we for different values of <span class="math inline">\(\lambda\)</span> to illustrate the effect:</p>
 <div class="cell" data-layout-align="center" data-hash="regularization_cache/html/unnamed-chunk-26_b9a1a97986e3cbf4854587c4d64238bb">
 <div class="sourceCode" id="cb23"><pre class="downlit sourceCode r code-with-copy"><code class="sourceCode R"><span><span class="va">n</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>
 <span><span class="va">sums</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="va">y</span> <span class="op">-</span> <span class="va">mu</span> <span class="op">-</span> <span class="va">a</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>

diff --git a/docs/index.html b/docs/index.html
@@ -352,7 +352,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="./ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>

diff --git a/docs/inference/bayes.html b/docs/inference/bayes.html
@@ -373,7 +373,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="../ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>

diff --git a/docs/inference/bootstrap.html b/docs/inference/bootstrap.html
@@ -373,7 +373,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="../ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>

diff --git a/docs/inference/bootstrap_files/figure-html/income-distribution-1.png b/docs/inference/bootstrap_files/figure-html/income-distribution-1.png
diff --git a/docs/inference/bootstrap_files/figure-html/median-is-normal-1.png b/docs/inference/bootstrap_files/figure-html/median-is-normal-1.png
diff --git a/docs/inference/clt.html b/docs/inference/clt.html
@@ -373,7 +373,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="../ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>

diff --git a/docs/inference/confidence-intervals.html b/docs/inference/confidence-intervals.html
@@ -373,7 +373,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="../ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>

diff --git a/docs/inference/hierarchical-models.html b/docs/inference/hierarchical-models.html
@@ -374,7 +374,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="../ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>

diff --git a/docs/inference/hypothesis-testing.html b/docs/inference/hypothesis-testing.html
@@ -373,7 +373,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="../ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>

diff --git a/docs/inference/intro-inference.html b/docs/inference/intro-inference.html
@@ -353,7 +353,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="../ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>

diff --git a/docs/inference/models.html b/docs/inference/models.html
@@ -373,7 +373,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="../ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>

diff --git a/docs/inference/parameters-estimates.html b/docs/inference/parameters-estimates.html
@@ -374,7 +374,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="../ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>

diff --git a/docs/intro.html b/docs/intro.html
@@ -353,7 +353,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="./ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>

diff --git a/docs/linear-models/association-not-causation.html b/docs/linear-models/association-not-causation.html
@@ -373,7 +373,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="../ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>

diff --git a/docs/linear-models/association-tests.html b/docs/linear-models/association-tests.html
@@ -374,7 +374,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="../ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>

diff --git a/docs/linear-models/intro-to-linear-models.html b/docs/linear-models/intro-to-linear-models.html
@@ -353,7 +353,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="../ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>

diff --git a/docs/linear-models/measurement-error-models.html b/docs/linear-models/measurement-error-models.html
@@ -373,7 +373,7 @@
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="../ml/cross-validation.html" class="sidebar-item-text sidebar-link">
+  <a href="../ml/resampling-methods.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">29</span>&nbsp; <span class="chapter-title">Resampling methods</span></span></a>
   </div>
 </li>