Building meaningful machine learning models for disease prediction

Posted on March 30, 2017 by Shirin's playgRound in R bloggers | 0 Comments

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Webinar for the ISDS R Group

This document presents the code I used to produce the example analysis and figures shown in my webinar on building meaningful machine learning models for disease prediction.

My webinar slides are available on Github

Description: Dr Shirin Glander will go over her work on building machine-learning models to predict the course of different diseases. She will go over building a model, evaluating its performance, and answering or addressing different disease related questions using machine learning. Her talk will cover the theory of machine learning as it is applied using R.

Setup

All analyses are done in R using RStudio. For detailed session information including R version, operating system and package versions, see the sessionInfo() output at the end of this document.

All figures are produced with ggplot2.

The dataset

The dataset I am using in these example analyses, is the Breast Cancer Wisconsin (Diagnostic) Dataset. The data was downloaded from the UC Irvine Machine Learning Repository.

The first dataset looks at the predictor classes:

  • malignant or
  • benign breast mass.

The features characterize cell nucleus properties and were generated from image analysis of fine needle aspirates (FNA) of breast masses:

  • Sample ID (code number)
  • Clump thickness
  • Uniformity of cell size
  • Uniformity of cell shape
  • Marginal adhesion
  • Single epithelial cell size
  • Number of bare nuclei
  • Bland chromatin
  • Number of normal nuclei
  • Mitosis
  • Classes, i.e. diagnosis
<span class="n">bc_data</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">read.table</span><span class="p">(</span><span class="s2">"datasets/breast-cancer-wisconsin.data.txt"</span><span class="p">,</span><span class="w"> 
                      </span><span class="n">header</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">FALSE</span><span class="p">,</span><span class="w"> 
                      </span><span class="n">sep</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">","</span><span class="p">)</span><span class="w">
</span><span class="n">colnames</span><span class="p">(</span><span class="n">bc_data</span><span class="p">)</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="nf">c</span><span class="p">(</span><span class="s2">"sample_code_number"</span><span class="p">,</span><span class="w"> 
                       </span><span class="s2">"clump_thickness"</span><span class="p">,</span><span class="w"> 
                       </span><span class="s2">"uniformity_of_cell_size"</span><span class="p">,</span><span class="w"> 
                       </span><span class="s2">"uniformity_of_cell_shape"</span><span class="p">,</span><span class="w"> 
                       </span><span class="s2">"marginal_adhesion"</span><span class="p">,</span><span class="w"> 
                       </span><span class="s2">"single_epithelial_cell_size"</span><span class="p">,</span><span class="w"> 
                       </span><span class="s2">"bare_nuclei"</span><span class="p">,</span><span class="w"> 
                       </span><span class="s2">"bland_chromatin"</span><span class="p">,</span><span class="w"> 
                       </span><span class="s2">"normal_nucleoli"</span><span class="p">,</span><span class="w"> 
                       </span><span class="s2">"mitosis"</span><span class="p">,</span><span class="w"> 
                       </span><span class="s2">"classes"</span><span class="p">)</span><span class="w">

</span><span class="n">bc_data</span><span class="o">$</span><span class="n">classes</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">ifelse</span><span class="p">(</span><span class="n">bc_data</span><span class="o">$</span><span class="n">classes</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="s2">"2"</span><span class="p">,</span><span class="w"> </span><span class="s2">"benign"</span><span class="p">,</span><span class="w">
                          </span><span class="n">ifelse</span><span class="p">(</span><span class="n">bc_data</span><span class="o">$</span><span class="n">classes</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="s2">"4"</span><span class="p">,</span><span class="w"> </span><span class="s2">"malignant"</span><span class="p">,</span><span class="w"> </span><span class="kc">NA</span><span class="p">))</span><span class="w">
</span>

Missing data

<span class="n">bc_data</span><span class="p">[</span><span class="n">bc_data</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="s2">"?"</span><span class="p">]</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="kc">NA</span><span class="w">

</span><span class="c1"># how many NAs are in the data
</span><span class="nf">length</span><span class="p">(</span><span class="n">which</span><span class="p">(</span><span class="nf">is.na</span><span class="p">(</span><span class="n">bc_data</span><span class="p">)))</span><span class="w">
</span>
## [1] 16
<span class="c1"># how many samples would we loose, if we removed them?
</span><span class="n">nrow</span><span class="p">(</span><span class="n">bc_data</span><span class="p">)</span><span class="w">
</span>
## [1] 699
<span class="n">nrow</span><span class="p">(</span><span class="n">bc_data</span><span class="p">[</span><span class="nf">is.na</span><span class="p">(</span><span class="n">bc_data</span><span class="p">),</span><span class="w"> </span><span class="p">])</span><span class="w">
</span>
## [1] 16

Missing values are imputed with the mice package.

<span class="c1"># impute missing data
</span><span class="n">library</span><span class="p">(</span><span class="n">mice</span><span class="p">)</span><span class="w">

</span><span class="n">bc_data</span><span class="p">[,</span><span class="m">2</span><span class="o">:</span><span class="m">10</span><span class="p">]</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">apply</span><span class="p">(</span><span class="n">bc_data</span><span class="p">[,</span><span class="w"> </span><span class="m">2</span><span class="o">:</span><span class="m">10</span><span class="p">],</span><span class="w"> </span><span class="m">2</span><span class="p">,</span><span class="w"> </span><span class="k">function</span><span class="p">(</span><span class="n">x</span><span class="p">)</span><span class="w"> </span><span class="nf">as.numeric</span><span class="p">(</span><span class="nf">as.character</span><span class="p">(</span><span class="n">x</span><span class="p">)))</span><span class="w">
</span><span class="n">dataset_impute</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">mice</span><span class="p">(</span><span class="n">bc_data</span><span class="p">[,</span><span class="w"> </span><span class="m">2</span><span class="o">:</span><span class="m">10</span><span class="p">],</span><span class="w">  </span><span class="n">print</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">FALSE</span><span class="p">)</span><span class="w">
</span><span class="n">bc_data</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">cbind</span><span class="p">(</span><span class="n">bc_data</span><span class="p">[,</span><span class="w"> </span><span class="m">11</span><span class="p">,</span><span class="w"> </span><span class="n">drop</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">FALSE</span><span class="p">],</span><span class="w"> </span><span class="n">mice</span><span class="o">::</span><span class="n">complete</span><span class="p">(</span><span class="n">dataset_impute</span><span class="p">,</span><span class="w"> </span><span class="m">1</span><span class="p">))</span><span class="w">

</span><span class="n">bc_data</span><span class="o">$</span><span class="n">classes</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">as.factor</span><span class="p">(</span><span class="n">bc_data</span><span class="o">$</span><span class="n">classes</span><span class="p">)</span><span class="w">

</span><span class="c1"># how many benign and malignant cases are there?
</span><span class="n">summary</span><span class="p">(</span><span class="n">bc_data</span><span class="o">$</span><span class="n">classes</span><span class="p">)</span><span class="w">
</span>

Data exploration

  • Response variable for classification
<span class="n">library</span><span class="p">(</span><span class="n">ggplot2</span><span class="p">)</span><span class="w">

</span><span class="n">ggplot</span><span class="p">(</span><span class="n">bc_data</span><span class="p">,</span><span class="w"> </span><span class="n">aes</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">classes</span><span class="p">,</span><span class="w"> </span><span class="n">fill</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">classes</span><span class="p">))</span><span class="w"> </span><span class="o">+</span><span class="w">
  </span><span class="n">geom_bar</span><span class="p">()</span><span class="w">
</span>

  • Response variable for regression
<span class="n">ggplot</span><span class="p">(</span><span class="n">bc_data</span><span class="p">,</span><span class="w"> </span><span class="n">aes</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">clump_thickness</span><span class="p">))</span><span class="w"> </span><span class="o">+</span><span class="w">
  </span><span class="n">geom_histogram</span><span class="p">(</span><span class="n">bins</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">10</span><span class="p">)</span><span class="w">
</span>

  • Principal Component Analysis
<span class="n">library</span><span class="p">(</span><span class="n">pcaGoPromoter</span><span class="p">)</span><span class="w">
</span><span class="n">library</span><span class="p">(</span><span class="n">ellipse</span><span class="p">)</span><span class="w">

</span><span class="c1"># perform pca and extract scores
</span><span class="n">pcaOutput</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">pca</span><span class="p">(</span><span class="n">t</span><span class="p">(</span><span class="n">bc_data</span><span class="p">[,</span><span class="w"> </span><span class="m">-1</span><span class="p">]),</span><span class="w"> </span><span class="n">printDropped</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">FALSE</span><span class="p">,</span><span class="w"> </span><span class="n">scale</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">TRUE</span><span class="p">,</span><span class="w"> </span><span class="n">center</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">TRUE</span><span class="p">)</span><span class="w">
</span><span class="n">pcaOutput2</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">as.data.frame</span><span class="p">(</span><span class="n">pcaOutput</span><span class="o">$</span><span class="n">scores</span><span class="p">)</span><span class="w">
  
</span><span class="c1"># define groups for plotting
</span><span class="n">pcaOutput2</span><span class="o">$</span><span class="n">groups</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">bc_data</span><span class="o">$</span><span class="n">classes</span><span class="w">
  
</span><span class="n">centroids</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">aggregate</span><span class="p">(</span><span class="n">cbind</span><span class="p">(</span><span class="n">PC1</span><span class="p">,</span><span class="w"> </span><span class="n">PC2</span><span class="p">)</span><span class="w"> </span><span class="o">~</span><span class="w"> </span><span class="n">groups</span><span class="p">,</span><span class="w"> </span><span class="n">pcaOutput2</span><span class="p">,</span><span class="w"> </span><span class="n">mean</span><span class="p">)</span><span class="w">

</span><span class="n">conf.rgn</span><span class="w">  </span><span class="o"><-</span><span class="w"> </span><span class="n">do.call</span><span class="p">(</span><span class="n">rbind</span><span class="p">,</span><span class="w"> </span><span class="n">lapply</span><span class="p">(</span><span class="n">unique</span><span class="p">(</span><span class="n">pcaOutput2</span><span class="o">$</span><span class="n">groups</span><span class="p">),</span><span class="w"> </span><span class="k">function</span><span class="p">(</span><span class="n">t</span><span class="p">)</span><span class="w">
  </span><span class="n">data.frame</span><span class="p">(</span><span class="n">groups</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nf">as.character</span><span class="p">(</span><span class="n">t</span><span class="p">),</span><span class="w">
             </span><span class="n">ellipse</span><span class="p">(</span><span class="n">cov</span><span class="p">(</span><span class="n">pcaOutput2</span><span class="p">[</span><span class="n">pcaOutput2</span><span class="o">$</span><span class="n">groups</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="n">t</span><span class="p">,</span><span class="w"> </span><span class="m">1</span><span class="o">:</span><span class="m">2</span><span class="p">]),</span><span class="w">
                   </span><span class="n">centre</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">as.matrix</span><span class="p">(</span><span class="n">centroids</span><span class="p">[</span><span class="n">centroids</span><span class="o">$</span><span class="n">groups</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="n">t</span><span class="p">,</span><span class="w"> </span><span class="m">2</span><span class="o">:</span><span class="m">3</span><span class="p">]),</span><span class="w">
                   </span><span class="n">level</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">0.95</span><span class="p">),</span><span class="w">
             </span><span class="n">stringsAsFactors</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">FALSE</span><span class="p">)))</span><span class="w">
    
</span><span class="n">ggplot</span><span class="p">(</span><span class="n">data</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">pcaOutput2</span><span class="p">,</span><span class="w"> </span><span class="n">aes</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">PC1</span><span class="p">,</span><span class="w"> </span><span class="n">y</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">PC2</span><span class="p">,</span><span class="w"> </span><span class="n">group</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">groups</span><span class="p">,</span><span class="w"> </span><span class="n">color</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">groups</span><span class="p">))</span><span class="w"> </span><span class="o">+</span><span class="w"> 
    </span><span class="n">geom_polygon</span><span class="p">(</span><span class="n">data</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">conf.rgn</span><span class="p">,</span><span class="w"> </span><span class="n">aes</span><span class="p">(</span><span class="n">fill</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">groups</span><span class="p">),</span><span class="w"> </span><span class="n">alpha</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">0.2</span><span class="p">)</span><span class="w"> </span><span class="o">+</span><span class="w">
    </span><span class="n">geom_point</span><span class="p">(</span><span class="n">size</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">2</span><span class="p">,</span><span class="w"> </span><span class="n">alpha</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">0.6</span><span class="p">)</span><span class="w"> </span><span class="o">+</span><span class="w"> 
    </span><span class="n">scale_color_brewer</span><span class="p">(</span><span class="n">palette</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"Set1"</span><span class="p">)</span><span class="w"> </span><span class="o">+</span><span class="w">
    </span><span class="n">labs</span><span class="p">(</span><span class="n">color</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">""</span><span class="p">,</span><span class="w">
         </span><span class="n">fill</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">""</span><span class="p">,</span><span class="w">
         </span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">paste0</span><span class="p">(</span><span class="s2">"PC1: "</span><span class="p">,</span><span class="w"> </span><span class="nf">round</span><span class="p">(</span><span class="n">pcaOutput</span><span class="o">$</span><span class="n">pov</span><span class="p">[</span><span class="m">1</span><span class="p">],</span><span class="w"> </span><span class="n">digits</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">2</span><span class="p">)</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="m">100</span><span class="p">,</span><span class="w"> </span><span class="s2">"% variance"</span><span class="p">),</span><span class="w">
         </span><span class="n">y</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">paste0</span><span class="p">(</span><span class="s2">"PC2: "</span><span class="p">,</span><span class="w"> </span><span class="nf">round</span><span class="p">(</span><span class="n">pcaOutput</span><span class="o">$</span><span class="n">pov</span><span class="p">[</span><span class="m">2</span><span class="p">],</span><span class="w"> </span><span class="n">digits</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">2</span><span class="p">)</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="m">100</span><span class="p">,</span><span class="w"> </span><span class="s2">"% variance"</span><span class="p">))</span><span class="w"> 
</span>

  • Features
<span class="n">library</span><span class="p">(</span><span class="n">tidyr</span><span class="p">)</span><span class="w">

</span><span class="n">gather</span><span class="p">(</span><span class="n">bc_data</span><span class="p">,</span><span class="w"> </span><span class="n">x</span><span class="p">,</span><span class="w"> </span><span class="n">y</span><span class="p">,</span><span class="w"> </span><span class="n">clump_thickness</span><span class="o">:</span><span class="n">mitosis</span><span class="p">)</span><span class="w"> </span><span class="o">%>%</span><span class="w">
  </span><span class="n">ggplot</span><span class="p">(</span><span class="n">aes</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">y</span><span class="p">,</span><span class="w"> </span><span class="n">color</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">classes</span><span class="p">,</span><span class="w"> </span><span class="n">fill</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">classes</span><span class="p">))</span><span class="w"> </span><span class="o">+</span><span class="w">
    </span><span class="n">geom_density</span><span class="p">(</span><span class="n">alpha</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">0.3</span><span class="p">)</span><span class="w"> </span><span class="o">+</span><span class="w">
    </span><span class="n">facet_wrap</span><span class="p">(</span><span class="w"> </span><span class="o">~</span><span class="w"> </span><span class="n">x</span><span class="p">,</span><span class="w"> </span><span class="n">scales</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"free"</span><span class="p">,</span><span class="w"> </span><span class="n">ncol</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">3</span><span class="p">)</span><span class="w">
</span>

Machine Learning packages for R

caret

<span class="c1"># configure multicore
</span><span class="n">library</span><span class="p">(</span><span class="n">doParallel</span><span class="p">)</span><span class="w">
</span><span class="n">cl</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">makeCluster</span><span class="p">(</span><span class="n">detectCores</span><span class="p">())</span><span class="w">
</span><span class="n">registerDoParallel</span><span class="p">(</span><span class="n">cl</span><span class="p">)</span><span class="w">

</span><span class="n">library</span><span class="p">(</span><span class="n">caret</span><span class="p">)</span><span class="w">
</span>

Training, validation and test data

<span class="n">set.seed</span><span class="p">(</span><span class="m">42</span><span class="p">)</span><span class="w">
</span><span class="n">index</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">createDataPartition</span><span class="p">(</span><span class="n">bc_data</span><span class="o">$</span><span class="n">classes</span><span class="p">,</span><span class="w"> </span><span class="n">p</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">0.7</span><span class="p">,</span><span class="w"> </span><span class="n">list</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">FALSE</span><span class="p">)</span><span class="w">
</span><span class="n">train_data</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">bc_data</span><span class="p">[</span><span class="n">index</span><span class="p">,</span><span class="w"> </span><span class="p">]</span><span class="w">
</span><span class="n">test_data</span><span class="w">  </span><span class="o"><-</span><span class="w"> </span><span class="n">bc_data</span><span class="p">[</span><span class="o">-</span><span class="n">index</span><span class="p">,</span><span class="w"> </span><span class="p">]</span><span class="w">
</span>
<span class="n">library</span><span class="p">(</span><span class="n">dplyr</span><span class="p">)</span><span class="w">

</span><span class="n">rbind</span><span class="p">(</span><span class="n">data.frame</span><span class="p">(</span><span class="n">group</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"train"</span><span class="p">,</span><span class="w"> </span><span class="n">train_data</span><span class="p">),</span><span class="w">
      </span><span class="n">data.frame</span><span class="p">(</span><span class="n">group</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"test"</span><span class="p">,</span><span class="w"> </span><span class="n">test_data</span><span class="p">))</span><span class="w"> </span><span class="o">%>%</span><span class="w">
  </span><span class="n">gather</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="w"> </span><span class="n">y</span><span class="p">,</span><span class="w"> </span><span class="n">clump_thickness</span><span class="o">:</span><span class="n">mitosis</span><span class="p">)</span><span class="w"> </span><span class="o">%>%</span><span class="w">
  </span><span class="n">ggplot</span><span class="p">(</span><span class="n">aes</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">y</span><span class="p">,</span><span class="w"> </span><span class="n">color</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">group</span><span class="p">,</span><span class="w"> </span><span class="n">fill</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">group</span><span class="p">))</span><span class="w"> </span><span class="o">+</span><span class="w">
    </span><span class="n">geom_density</span><span class="p">(</span><span class="n">alpha</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">0.3</span><span class="p">)</span><span class="w"> </span><span class="o">+</span><span class="w">
    </span><span class="n">facet_wrap</span><span class="p">(</span><span class="w"> </span><span class="o">~</span><span class="w"> </span><span class="n">x</span><span class="p">,</span><span class="w"> </span><span class="n">scales</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"free"</span><span class="p">,</span><span class="w"> </span><span class="n">ncol</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">3</span><span class="p">)</span><span class="w">
</span>

Regression

<span class="n">set.seed</span><span class="p">(</span><span class="m">42</span><span class="p">)</span><span class="w">
</span><span class="n">model_glm</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">caret</span><span class="o">::</span><span class="n">train</span><span class="p">(</span><span class="n">clump_thickness</span><span class="w"> </span><span class="o">~</span><span class="w"> </span><span class="n">.</span><span class="p">,</span><span class="w">
                          </span><span class="n">data</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">train_data</span><span class="p">,</span><span class="w">
                          </span><span class="n">method</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"glm"</span><span class="p">,</span><span class="w">
                          </span><span class="n">preProcess</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nf">c</span><span class="p">(</span><span class="s2">"scale"</span><span class="p">,</span><span class="w"> </span><span class="s2">"center"</span><span class="p">),</span><span class="w">
                          </span><span class="n">trControl</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">trainControl</span><span class="p">(</span><span class="n">method</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"repeatedcv"</span><span class="p">,</span><span class="w"> 
                                                  </span><span class="n">number</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">10</span><span class="p">,</span><span class="w"> 
                                                  </span><span class="n">repeats</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">10</span><span class="p">,</span><span class="w"> 
                                                  </span><span class="n">savePredictions</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">TRUE</span><span class="p">,</span><span class="w"> 
                                                  </span><span class="n">verboseIter</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">FALSE</span><span class="p">))</span><span class="w">
</span>
<span class="n">model_glm</span><span class="w">
</span>
## Generalized Linear Model 
## 
## 490 samples
##   9 predictor
## 
## Pre-processing: scaled (9), centered (9) 
## Resampling: Cross-Validated (10 fold, repeated 10 times) 
## Summary of sample sizes: 441, 441, 440, 442, 441, 440, ... 
## Resampling results:
## 
##   RMSE      Rsquared 
##   1.974296  0.5016141
## 
##
<span class="n">predictions</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">predict</span><span class="p">(</span><span class="n">model_glm</span><span class="p">,</span><span class="w"> </span><span class="n">test_data</span><span class="p">)</span><span class="w">
</span>
<span class="c1"># model_glm$finalModel$linear.predictors == model_glm$finalModel$fitted.values
</span><span class="n">data.frame</span><span class="p">(</span><span class="n">residuals</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">resid</span><span class="p">(</span><span class="n">model_glm</span><span class="p">),</span><span class="w">
           </span><span class="n">predictors</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">model_glm</span><span class="o">$</span><span class="n">finalModel</span><span class="o">$</span><span class="n">linear.predictors</span><span class="p">)</span><span class="w"> </span><span class="o">%>%</span><span class="w">
  </span><span class="n">ggplot</span><span class="p">(</span><span class="n">aes</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">predictors</span><span class="p">,</span><span class="w"> </span><span class="n">y</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">residuals</span><span class="p">))</span><span class="w"> </span><span class="o">+</span><span class="w">
    </span><span class="n">geom_jitter</span><span class="p">()</span><span class="w"> </span><span class="o">+</span><span class="w">
    </span><span class="n">geom_smooth</span><span class="p">(</span><span class="n">method</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"lm"</span><span class="p">)</span><span class="w">
</span>

<span class="c1"># y == train_data$clump_thickness
</span><span class="n">data.frame</span><span class="p">(</span><span class="n">residuals</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">resid</span><span class="p">(</span><span class="n">model_glm</span><span class="p">),</span><span class="w">
           </span><span class="n">y</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">model_glm</span><span class="o">$</span><span class="n">finalModel</span><span class="o">$</span><span class="n">y</span><span class="p">)</span><span class="w"> </span><span class="o">%>%</span><span class="w">
  </span><span class="n">ggplot</span><span class="p">(</span><span class="n">aes</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">y</span><span class="p">,</span><span class="w"> </span><span class="n">y</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">residuals</span><span class="p">))</span><span class="w"> </span><span class="o">+</span><span class="w">
    </span><span class="n">geom_jitter</span><span class="p">()</span><span class="w"> </span><span class="o">+</span><span class="w">
    </span><span class="n">geom_smooth</span><span class="p">(</span><span class="n">method</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"lm"</span><span class="p">)</span><span class="w">
</span>

<span class="n">data.frame</span><span class="p">(</span><span class="n">actual</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">test_data</span><span class="o">$</span><span class="n">clump_thickness</span><span class="p">,</span><span class="w">
           </span><span class="n">predicted</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">predictions</span><span class="p">)</span><span class="w"> </span><span class="o">%>%</span><span class="w">
  </span><span class="n">ggplot</span><span class="p">(</span><span class="n">aes</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">actual</span><span class="p">,</span><span class="w"> </span><span class="n">y</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">predicted</span><span class="p">))</span><span class="w"> </span><span class="o">+</span><span class="w">
    </span><span class="n">geom_jitter</span><span class="p">()</span><span class="w"> </span><span class="o">+</span><span class="w">
    </span><span class="n">geom_smooth</span><span class="p">(</span><span class="n">method</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"lm"</span><span class="p">)</span><span class="w">
</span>

Classification

Decision trees

rpart

<span class="n">library</span><span class="p">(</span><span class="n">rpart</span><span class="p">)</span><span class="w">
</span><span class="n">library</span><span class="p">(</span><span class="n">rpart.plot</span><span class="p">)</span><span class="w">

</span><span class="n">set.seed</span><span class="p">(</span><span class="m">42</span><span class="p">)</span><span class="w">
</span><span class="n">fit</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">rpart</span><span class="p">(</span><span class="n">classes</span><span class="w"> </span><span class="o">~</span><span class="w"> </span><span class="n">.</span><span class="p">,</span><span class="w">
            </span><span class="n">data</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">train_data</span><span class="p">,</span><span class="w">
            </span><span class="n">method</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"class"</span><span class="p">,</span><span class="w">
            </span><span class="n">control</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">rpart.control</span><span class="p">(</span><span class="n">xval</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">10</span><span class="p">,</span><span class="w"> 
                                    </span><span class="n">minbucket</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">2</span><span class="p">,</span><span class="w"> 
                                    </span><span class="n">cp</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">0</span><span class="p">),</span><span class="w"> 
             </span><span class="n">parms</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nf">list</span><span class="p">(</span><span class="n">split</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"information"</span><span class="p">))</span><span class="w">

</span><span class="n">rpart.plot</span><span class="p">(</span><span class="n">fit</span><span class="p">,</span><span class="w"> </span><span class="n">extra</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">100</span><span class="p">)</span><span class="w">
</span>

Random Forests

Random Forests predictions are based on the generation of multiple classification trees. They can be used for both, classification and regression tasks. Here, I show a classification task.

<span class="n">set.seed</span><span class="p">(</span><span class="m">42</span><span class="p">)</span><span class="w">
</span><span class="n">model_rf</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">caret</span><span class="o">::</span><span class="n">train</span><span class="p">(</span><span class="n">classes</span><span class="w"> </span><span class="o">~</span><span class="w"> </span><span class="n">.</span><span class="p">,</span><span class="w">
                         </span><span class="n">data</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">train_data</span><span class="p">,</span><span class="w">
                         </span><span class="n">method</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"rf"</span><span class="p">,</span><span class="w">
                         </span><span class="n">preProcess</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nf">c</span><span class="p">(</span><span class="s2">"scale"</span><span class="p">,</span><span class="w"> </span><span class="s2">"center"</span><span class="p">),</span><span class="w">
                         </span><span class="n">trControl</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">trainControl</span><span class="p">(</span><span class="n">method</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"repeatedcv"</span><span class="p">,</span><span class="w"> 
                                                  </span><span class="n">number</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">10</span><span class="p">,</span><span class="w"> 
                                                  </span><span class="n">repeats</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">10</span><span class="p">,</span><span class="w"> 
                                                  </span><span class="n">savePredictions</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">TRUE</span><span class="p">,</span><span class="w"> 
                                                  </span><span class="n">verboseIter</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">FALSE</span><span class="p">))</span><span class="w">
</span>

When you specify savePredictions = TRUE, you can access the cross-validation resuls with model_rf$pred.

<span class="n">model_rf</span><span class="o">$</span><span class="n">finalModel</span><span class="o">$</span><span class="n">confusion</span><span class="w">
</span>
##           benign malignant class.error
## benign       313         8  0.02492212
## malignant      4       165  0.02366864

  • Feature Importance
<span class="n">imp</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">model_rf</span><span class="o">$</span><span class="n">finalModel</span><span class="o">$</span><span class="n">importance</span><span class="w">
</span><span class="n">imp</span><span class="p">[</span><span class="n">order</span><span class="p">(</span><span class="n">imp</span><span class="p">,</span><span class="w"> </span><span class="n">decreasing</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">TRUE</span><span class="p">),</span><span class="w"> </span><span class="p">]</span><span class="w">
</span>
##     uniformity_of_cell_size    uniformity_of_cell_shape 
##                   54.416003                   41.553022 
##             bland_chromatin                 bare_nuclei 
##                   29.343027                   28.483842 
##             normal_nucleoli single_epithelial_cell_size 
##                   19.239635                   18.480155 
##             clump_thickness           marginal_adhesion 
##                   13.276702                   12.143355 
##                     mitosis 
##                    3.081635
<span class="c1"># estimate variable importance
</span><span class="n">importance</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">varImp</span><span class="p">(</span><span class="n">model_rf</span><span class="p">,</span><span class="w"> </span><span class="n">scale</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">TRUE</span><span class="p">)</span><span class="w">
</span><span class="n">plot</span><span class="p">(</span><span class="n">importance</span><span class="p">)</span><span class="w">
</span>

  • predicting test data
<span class="n">confusionMatrix</span><span class="p">(</span><span class="n">predict</span><span class="p">(</span><span class="n">model_rf</span><span class="p">,</span><span class="w"> </span><span class="n">test_data</span><span class="p">),</span><span class="w"> </span><span class="n">test_data</span><span class="o">$</span><span class="n">classes</span><span class="p">)</span><span class="w">
</span>
## Confusion Matrix and Statistics
## 
##            Reference
## Prediction  benign malignant
##   benign       133         2
##   malignant      4        70
##                                           
##                Accuracy : 0.9713          
##                  95% CI : (0.9386, 0.9894)
##     No Information Rate : 0.6555          
##     P-Value [Acc > NIR] : <2e-16          
##                                           
##                   Kappa : 0.9369          
##  Mcnemar's Test P-Value : 0.6831          
##                                           
##             Sensitivity : 0.9708          
##             Specificity : 0.9722          
##          Pos Pred Value : 0.9852          
##          Neg Pred Value : 0.9459          
##              Prevalence : 0.6555          
##          Detection Rate : 0.6364          
##    Detection Prevalence : 0.6459          
##       Balanced Accuracy : 0.9715          
##                                           
##        'Positive' Class : benign          
##
<span class="n">results</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">data.frame</span><span class="p">(</span><span class="n">actual</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">test_data</span><span class="o">$</span><span class="n">classes</span><span class="p">,</span><span class="w">
                      </span><span class="n">predict</span><span class="p">(</span><span class="n">model_rf</span><span class="p">,</span><span class="w"> </span><span class="n">test_data</span><span class="p">,</span><span class="w"> </span><span class="n">type</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"prob"</span><span class="p">))</span><span class="w">

</span><span class="n">results</span><span class="o">$</span><span class="n">prediction</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">ifelse</span><span class="p">(</span><span class="n">results</span><span class="o">$</span><span class="n">benign</span><span class="w"> </span><span class="o">></span><span class="w"> </span><span class="m">0.5</span><span class="p">,</span><span class="w"> </span><span class="s2">"benign"</span><span class="p">,</span><span class="w">
                             </span><span class="n">ifelse</span><span class="p">(</span><span class="n">results</span><span class="o">$</span><span class="n">malignant</span><span class="w"> </span><span class="o">></span><span class="w"> </span><span class="m">0.5</span><span class="p">,</span><span class="w"> </span><span class="s2">"malignant"</span><span class="p">,</span><span class="w"> </span><span class="kc">NA</span><span class="p">))</span><span class="w">

</span><span class="n">results</span><span class="o">$</span><span class="n">correct</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">ifelse</span><span class="p">(</span><span class="n">results</span><span class="o">$</span><span class="n">actual</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="n">results</span><span class="o">$</span><span class="n">prediction</span><span class="p">,</span><span class="w"> </span><span class="kc">TRUE</span><span class="p">,</span><span class="w"> </span><span class="kc">FALSE</span><span class="p">)</span><span class="w">

</span><span class="n">ggplot</span><span class="p">(</span><span class="n">results</span><span class="p">,</span><span class="w"> </span><span class="n">aes</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">prediction</span><span class="p">,</span><span class="w"> </span><span class="n">fill</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">correct</span><span class="p">))</span><span class="w"> </span><span class="o">+</span><span class="w">
  </span><span class="n">geom_bar</span><span class="p">(</span><span class="n">position</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"dodge"</span><span class="p">)</span><span class="w">
</span>

<span class="n">ggplot</span><span class="p">(</span><span class="n">results</span><span class="p">,</span><span class="w"> </span><span class="n">aes</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">prediction</span><span class="p">,</span><span class="w"> </span><span class="n">y</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">benign</span><span class="p">,</span><span class="w"> </span><span class="n">color</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">correct</span><span class="p">,</span><span class="w"> </span><span class="n">shape</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">correct</span><span class="p">))</span><span class="w"> </span><span class="o">+</span><span class="w">
  </span><span class="n">geom_jitter</span><span class="p">(</span><span class="n">size</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">3</span><span class="p">,</span><span class="w"> </span><span class="n">alpha</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">0.6</span><span class="p">)</span><span class="w">
</span>

Extreme gradient boosting trees

Extreme gradient boosting (XGBoost) is a faster and improved implementation of gradient boosting for supervised learning.

“XGBoost uses a more regularized model formalization to control over-fitting, which gives it better performance.” Tianqi Chen, developer of xgboost

XGBoost is a tree ensemble model, which means the sum of predictions from a set of classification and regression trees (CART). In that, XGBoost is similar to Random Forests but it uses a different approach to model training. Can be used for classification and regression tasks. Here, I show a classification task.

<span class="n">set.seed</span><span class="p">(</span><span class="m">42</span><span class="p">)</span><span class="w">
</span><span class="n">model_xgb</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">caret</span><span class="o">::</span><span class="n">train</span><span class="p">(</span><span class="n">classes</span><span class="w"> </span><span class="o">~</span><span class="w"> </span><span class="n">.</span><span class="p">,</span><span class="w">
                          </span><span class="n">data</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">train_data</span><span class="p">,</span><span class="w">
                          </span><span class="n">method</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"xgbTree"</span><span class="p">,</span><span class="w">
                          </span><span class="n">preProcess</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="nf">c</span><span class="p">(</span><span class="s2">"scale"</span><span class="p">,</span><span class="w"> </span><span class="s2">"center"</span><span class="p">),</span><span class="w">
                          </span><span class="n">trControl</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">trainControl</span><span class="p">(</span><span class="n">method</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"repeatedcv"</span><span class="p">,</span><span class="w"> 
                                                  </span><span class="n">number</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">10</span><span class="p">,</span><span class="w"> 
                                                  </span><span class="n">repeats</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="m">10</span><span class="p">,</span><span class="w"> 
                                                  </span><span class="n">savePredictions</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">TRUE</span><span class="p">,</span><span class="w"> 
                                                  </span><span class="n">verboseIter</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">FALSE</span><span class="p">))</span><span class="w">
</span>

  • Feature Importance
<span class="n">importance</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">varImp</span><span class="p">(</span><span class="n">model_xgb</span><span class="p">,</span><span class="w"> </span><span class="n">scale</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="kc">TRUE</span><span class="p">)</span><span class="w">
</span><span class="n">plot</span><span class="p">(</span><span class="n">importance</span><span class="p">)</span><span class="w">
</span>

  • predicting test data
<span class="n">confusionMatrix</span><span class="p">(</span><span class="n">predict</span><span class="p">(</span><span class="n">model_xgb</span><span class="p">,</span><span class="w"> </span><span class="n">test_data</span><span class="p">),</span><span class="w"> </span><span class="n">test_data</span><span class="o">$</span><span class="n">classes</span><span class="p">)</span><span class="w">
</span>
## Confusion Matrix and Statistics
## 
##            Reference
## Prediction  benign malignant
##   benign       132         2
##   malignant      5        70
##                                           
##                Accuracy : 0.9665          
##                  95% CI : (0.9322, 0.9864)
##     No Information Rate : 0.6555          
##     P-Value [Acc > NIR] : <2e-16          
##                                           
##                   Kappa : 0.9266          
##  Mcnemar's Test P-Value : 0.4497          
##                                           
##             Sensitivity : 0.9635          
##             Specificity : 0.9722          
##          Pos Pred Value : 0.9851          
##          Neg Pred Value : 0.9333          
##              Prevalence : 0.6555          
##          Detection Rate : 0.6316          
##    Detection Prevalence : 0.6411          
##       Balanced Accuracy : 0.9679          
##                                           
##        'Positive' Class : benign          
##
<span class="n">results</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">data.frame</span><span class="p">(</span><span class="n">actual</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">test_data</span><span class="o">$</span><span class="n">classes</span><span class="p">,</span><span class="w">
                      </span><span class="n">predict</span><span class="p">(</span><span class="n">model_xgb</span><span class="p">,</span><span class="w"> </span><span class="n">test_data</span><span class="p">,</span><span class="w"> </span><span class="n">type</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"prob"</span><span class="p">))</span><span class="w">

</span><span class="n">results</span><span class="o">$</span><span class="n">prediction</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">ifelse</span><span class="p">(</span><span class="n">results</span><span class="o">$</span><span class="n">benign</span><span class="w"> </span><span class="o">></span><span class="w"> </span><span class="m">0.5</span><span class="p">,</span><span class="w"> </span><span class="s2">"benign"</span><span class="p">,</span><span class="w">
                             </span><span class="n">ifelse</span><span class="p">(</span><span class="n">results</span><span class="o">$</span><span class="n">malignant</span><span class="w"> </span><span class="o">></span><span class="w"> </span><span class="m">0.5</span><span class="p">,</span><span class="w"> </span><span class="s2">"malignant"</span><span class="p">,</span><span class="w"> </span><span class="kc">NA</span><span class="p">))</span><span class="w">

</span><span class="n">results</span><span class="o">$</span><span class="n">correct</span><span class="w"> </span><span class="o"><-</span><span class="w"> </span><span class="n">ifelse</span><span class="p">(</span><span class="n">results</span><span class="o">$</span><span class="n">actual</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="n">results</span><span class="o">$</span><span class="n">prediction</span><span class="p">,</span><span class="w"> </span><span class="kc">TRUE</span><span class="p">,</span><span class="w"> </span><span class="kc">FALSE</span><span class="p">)</span><span class="w">

</span><span class="n">ggplot</span><span class="p">(</span><span class="n">results</span><span class="p">,</span><span class="w"> </span><span class="n">aes</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">prediction</span><span class="p">,</span><span class="w"> </span><span class="n">fill</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">correct</span><span class="p">))</span><span class="w"> </span><span class="o">+</span><span class="w">
  </span><span class="n">geom_bar</span><span class="p">(</span><span class="n">position</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">"dodge"</span><span class="p">)</span><span class="w">
</span>

<span class="n">ggplot</span><span class="p">(</span><span class="n">results</span><span class="p">,</span><span class="w"> </span><span class="n">aes</span><span class="p">(</span><span class="n">x</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">prediction</span><span class="p">,</span><span class="w"> </span><span class="n">y</span><span cla...

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