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Updated clustering.
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mhahsler committed Oct 16, 2024
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2 changes: 1 addition & 1 deletion book/404.html
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<p>"<strong>An R Companion for Introduction to Data Mining</strong>" was written by Michael Hahsler. It was last built on 2024-10-14.</p>
<p>"<strong>An R Companion for Introduction to Data Mining</strong>" was written by Michael Hahsler. It was last built on 2024-10-15.</p>
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2 changes: 1 addition & 1 deletion book/association-analysis-advanced-concepts.html
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Expand Up @@ -575,7 +575,7 @@ <h2>
<footer class="bg-primary text-light mt-5"><div class="container"><div class="row">

<div class="col-12 col-md-6 mt-3">
<p>"<strong>An R Companion for Introduction to Data Mining</strong>" was written by Michael Hahsler. It was last built on 2024-10-14.</p>
<p>"<strong>An R Companion for Introduction to Data Mining</strong>" was written by Michael Hahsler. It was last built on 2024-10-15.</p>
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12 changes: 6 additions & 6 deletions book/association-analysis-basic-concepts.html
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2 changes: 1 addition & 1 deletion book/classification-alternative-techniques.html
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Expand Up @@ -2238,7 +2238,7 @@ <h2>
<footer class="bg-primary text-light mt-5"><div class="container"><div class="row">

<div class="col-12 col-md-6 mt-3">
<p>"<strong>An R Companion for Introduction to Data Mining</strong>" was written by Michael Hahsler. It was last built on 2024-10-14.</p>
<p>"<strong>An R Companion for Introduction to Data Mining</strong>" was written by Michael Hahsler. It was last built on 2024-10-15.</p>
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4 changes: 2 additions & 2 deletions book/classification-basic-concepts.html
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Expand Up @@ -1147,7 +1147,7 @@ <h3>
<code class="sourceCode R"><span><span class="va">f</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/FSelector/man/as.simple.formula.html">as.simple.formula</a></span><span class="op">(</span><span class="va">subset</span>, <span class="st">"type"</span><span class="op">)</span></span>
<span><span class="va">f</span></span>
<span><span class="co">## type ~ feathers + milk + backbone + toothed + eggs</span></span>
<span><span class="co">## &lt;environment: 0x59dc899af2d0&gt;</span></span>
<span><span class="co">## &lt;environment: 0x56507134d810&gt;</span></span>
<span><span class="va">m</span> <span class="op">&lt;-</span> <span class="va">Zoo_train</span> <span class="op">|&gt;</span> <span class="fu"><a href="https://rdrr.io/pkg/rpart/man/rpart.html">rpart</a></span><span class="op">(</span><span class="va">f</span>, data <span class="op">=</span> <span class="va">_</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/pkg/rpart.plot/man/rpart.plot.html">rpart.plot</a></span><span class="op">(</span><span class="va">m</span>, extra <span class="op">=</span> <span class="fl">2</span>, roundint <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
<div class="inline-figure"><img src="R-Companion-Data-Mining_files/figure-html/unnamed-chunk-170-1.png" width="672"></div>
Expand Down Expand Up @@ -1404,7 +1404,7 @@ <h2>
<footer class="bg-primary text-light mt-5"><div class="container"><div class="row">

<div class="col-12 col-md-6 mt-3">
<p>"<strong>An R Companion for Introduction to Data Mining</strong>" was written by Michael Hahsler. It was last built on 2024-10-14.</p>
<p>"<strong>An R Companion for Introduction to Data Mining</strong>" was written by Michael Hahsler. It was last built on 2024-10-15.</p>
</div>

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35 changes: 18 additions & 17 deletions book/cluster-analysis.html
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Expand Up @@ -360,16 +360,12 @@ <h2>
<span><span class="fu"><a href="https://rdrr.io/pkg/factoextra/man/fviz_cluster.html">fviz_cluster</a></span><span class="op">(</span><span class="va">km</span>, data <span class="op">=</span> <span class="va">ruspini_scaled</span>, centroids <span class="op">=</span> <span class="cn">TRUE</span>, </span>
<span> repel <span class="op">=</span> <span class="cn">TRUE</span>, ellipse.type <span class="op">=</span> <span class="st">"norm"</span><span class="op">)</span></span></code></pre></div>
<div class="inline-figure"><img src="R-Companion-Data-Mining_files/figure-html/unnamed-chunk-324-1.png" width="672"></div>
<div id="inspect-clusters" class="section level4" number="7.2.0.1">
<h4>
<span class="header-section-number">7.2.0.1</span> Inspect clusters<a class="anchor" aria-label="anchor" href="#inspect-clusters"><i class="fas fa-link"></i></a>
</h4>
<div id="inspect-clusters" class="section level3" number="7.2.1">
<h3>
<span class="header-section-number">7.2.1</span> Inspect Clusters<a class="anchor" aria-label="anchor" href="#inspect-clusters"><i class="fas fa-link"></i></a>
</h3>
<p>We inspect the clusters created by the 4-cluster k-means solution. The
following code can be adapted to be used for other clustering methods.</p>
<div id="cluster-profiles" class="section level5" number="7.2.0.1.1">
<h5>
<span class="header-section-number">7.2.0.1.1</span> Cluster Profiles<a class="anchor" aria-label="anchor" href="#cluster-profiles"><i class="fas fa-link"></i></a>
</h5>
<p>Inspect the centroids with horizontal bar charts organized by cluster.
To group the plots by cluster, we have to change the data format to the
“long”-format using a pivot operation. I use colors to match the
Expand All @@ -378,15 +374,16 @@ <h5>
<code class="sourceCode R"><span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot</a></span><span class="op">(</span><span class="fu"><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">pivot_longer</a></span><span class="op">(</span><span class="va">centroids</span>, </span>
<span> cols <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span>, </span>
<span> names_to <span class="op">=</span> <span class="st">"feature"</span><span class="op">)</span>,</span>
<span> <span class="co">#aes(x = feature, y = value, fill = cluster)) +</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">value</span>, y <span class="op">=</span> <span class="va">feature</span>, fill <span class="op">=</span> <span class="va">cluster</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html">geom_bar</a></span><span class="op">(</span>stat <span class="op">=</span> <span class="st">"identity"</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/facet_grid.html">facet_grid</a></span><span class="op">(</span>rows <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html">vars</a></span><span class="op">(</span><span class="va">cluster</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<div class="inline-figure"><img src="R-Companion-Data-Mining_files/figure-html/unnamed-chunk-325-1.png" width="672"></div>
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/facet_grid.html">facet_grid</a></span><span class="op">(</span>cols <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/vars.html">vars</a></span><span class="op">(</span><span class="va">cluster</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<div class="inline-figure"><img src="R-Companion-Data-Mining_files/figure-html/unnamed-chunk-325-1.png" width="768"></div>
</div>
<div id="extract-a-single-cluster" class="section level5" number="7.2.0.1.2">
<h5>
<span class="header-section-number">7.2.0.1.2</span> Extract a single cluster<a class="anchor" aria-label="anchor" href="#extract-a-single-cluster"><i class="fas fa-link"></i></a>
</h5>
<div id="extract-a-single-cluster" class="section level3" number="7.2.2">
<h3>
<span class="header-section-number">7.2.2</span> Extract a Single Cluster<a class="anchor" aria-label="anchor" href="#extract-a-single-cluster"><i class="fas fa-link"></i></a>
</h3>
<p>You need is to filter the rows corresponding to the cluster index. The
next example calculates summary statistics and then plots all data
points of cluster 1.</p>
Expand Down Expand Up @@ -426,7 +423,6 @@ <h5>
<div class="inline-figure"><img src="R-Companion-Data-Mining_files/figure-html/unnamed-chunk-327-1.png" width="672"></div>
</div>
</div>
</div>
<div id="agglomerative-hierarchical-clustering" class="section level2" number="7.3">
<h2>
<span class="header-section-number">7.3</span> Agglomerative Hierarchical Clustering<a class="anchor" aria-label="anchor" href="#agglomerative-hierarchical-clustering"><i class="fas fa-link"></i></a>
Expand Down Expand Up @@ -1708,7 +1704,12 @@ <h2>
<li><a class="nav-link" href="#scale-data"><span class="header-section-number">7.1.3</span> Scale data</a></li>
</ul>
</li>
<li><a class="nav-link" href="#k-means"><span class="header-section-number">7.2</span> K-means</a></li>
<li>
<a class="nav-link" href="#k-means"><span class="header-section-number">7.2</span> K-means</a><ul class="nav navbar-nav">
<li><a class="nav-link" href="#inspect-clusters"><span class="header-section-number">7.2.1</span> Inspect Clusters</a></li>
<li><a class="nav-link" href="#extract-a-single-cluster"><span class="header-section-number">7.2.2</span> Extract a Single Cluster</a></li>
</ul>
</li>
<li>
<a class="nav-link" href="#agglomerative-hierarchical-clustering"><span class="header-section-number">7.3</span> Agglomerative Hierarchical Clustering</a><ul class="nav navbar-nav">
<li><a class="nav-link" href="#creating-a-dendrogram"><span class="header-section-number">7.3.1</span> Creating a Dendrogram</a></li>
Expand Down Expand Up @@ -1762,7 +1763,7 @@ <h2>
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<div class="col-12 col-md-6 mt-3">
<p>"<strong>An R Companion for Introduction to Data Mining</strong>" was written by Michael Hahsler. It was last built on 2024-10-14.</p>
<p>"<strong>An R Companion for Introduction to Data Mining</strong>" was written by Michael Hahsler. It was last built on 2024-10-15.</p>
</div>

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