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j1-template 2022.4.2 → 2022.4.3

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-<div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># HIDDEN</span>
-<span class="kn">from</span> <span class="nn">datascience</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="o">%</span><span class="k">matplotlib</span> inline
-<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plots</span>
-<span class="n">plots</span><span class="o">.</span><span class="n">style</span><span class="o">.</span><span class="n">use</span><span class="p">(</span><span class="s1">&#39;fivethirtyeight&#39;</span><span class="p">)</span>
-<span class="kn">import</span> <span class="nn">math</span>
-<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
-<span class="kn">from</span> <span class="nn">scipy</span> <span class="kn">import</span> <span class="n">stats</span>
-<span class="kn">from</span> <span class="nn">ipywidgets</span> <span class="kn">import</span> <span class="n">interact</span><span class="p">,</span> <span class="n">interactive</span><span class="p">,</span> <span class="n">fixed</span><span class="p">,</span> <span class="n">interact_manual</span>
-<span class="kn">import</span> <span class="nn">ipywidgets</span> <span class="k">as</span> <span class="nn">widgets</span>
-<span class="kn">import</span> <span class="nn">nbinteract</span> <span class="k">as</span> <span class="nn">nbi</span>
-</pre></div>
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-<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
-<div class="text_cell_render border-box-sizing rendered_html">
-<h3 id="Correlation">Correlation<a class="anchor-link" href="#Correlation">&#182;</a></h3><p>In this section we will develop a measure of how tightly clustered a scatter diagram is about a straight line. Formally, this is called measuring <em>linear association</em>.</p>
-</div>
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-<h4 id="The-correlation-coefficient">The correlation coefficient<a class="anchor-link" href="#The-correlation-coefficient">&#182;</a></h4><p>The <em>correlation coefficient</em> measures the strength of the linear relationship between two variables. Graphically, it measures how clustered the scatter diagram is around a straight line.</p>
-<p>The term <em>correlation coefficient</em> is a quite long word, so usually the term shortened to <em>correlation</em> and denoted by $r$.</p>
-<p>Here are some mathematical facts about $r$ that we will just observe by simulation.</p>
-<ul>
-<li>The correlation coefficient $r$ is a number between -1 and 1.</li>
-<li>$r$ measures the extent to which the scatter plot clusters around a straight line.</li>
-<li>$r$ = 1 if the scatter diagram is a perfect straight line sloping upwards, and $r$ = -1 if the scatter diagram is a perfect straight line sloping downwards.</li>
-</ul>
-</div>
-</div>
-</div>
-<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
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-<p>The function <code>r_scatter</code> takes a value of $r$ as its argument and simulates a scatter plot with a correlation very close to $r$. Because of randomness in the simulation, the correlation is not expected to be exactly equal to $r$.</p>
-<p>Call <code>r_scatter</code> a few times, with different values of $r$ as the argument, and see how the scatter plot changes.</p>
-<p>When $r$ = 1 the scatter plot is perfectly linear and slopes upward. When $r$ = -1, the scatter plot is perfectly linear and slopes downward. When $r$ = 0, the scatter plot is a formless cloud around the horizontal axis, and the variables are said to be <em>uncorrelated</em>.</p>
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-<div class=" highlight hl-ipython3"><pre><span></span><span class="n">z</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">normal</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">500</span><span class="p">)</span>
-<span class="k">def</span> <span class="nf">r_scatter</span><span class="p">(</span><span class="n">xs</span><span class="p">,</span> <span class="n">r</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">    Generate y-values for a scatter plot with correlation approximately r</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">return</span> <span class="n">r</span><span class="o">*</span><span class="n">xs</span> <span class="o">+</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="mi">1</span><span class="o">-</span><span class="n">r</span><span class="o">**</span><span class="mi">2</span><span class="p">))</span><span class="o">*</span><span class="n">z</span>
-<span class="n">corr_opts</span> <span class="o">=</span> <span class="p">{</span>
-    <span class="s1">&#39;aspect_ratio&#39;</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
-    <span class="s1">&#39;xlim&#39;</span><span class="p">:</span> <span class="p">(</span><span class="o">-</span><span class="mf">3.5</span><span class="p">,</span> <span class="mf">3.5</span><span class="p">),</span>
-    <span class="s1">&#39;ylim&#39;</span><span class="p">:</span> <span class="p">(</span><span class="o">-</span><span class="mf">3.5</span><span class="p">,</span> <span class="mf">3.5</span><span class="p">),</span>
-<span class="p">}</span>
-<span class="n">nbi</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">normal</span><span class="p">(</span><span class="n">size</span><span class="o">=</span><span class="mi">500</span><span class="p">),</span> <span class="n">r_scatter</span><span class="p">,</span> <span class="n">options</span><span class="o">=</span><span class="n">corr_opts</span><span class="p">,</span> <span class="n">r</span><span class="o">=</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mf">0.05</span><span class="p">))</span>
-</pre></div>
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-<h4 id="Calculating-the-correlation">Calculating the correlation<a class="anchor-link" href="#Calculating-the-correlation">&#182;</a></h4><p>The formula for $r$ is not apparent from our observations so far. It has a mathematical basis that is outside the scope of this class. However, as you will see, the calculation is straightforward and helps us understand several of the properties of $r$.</p>
-<p><strong>Formula</strong> for $r$:</p>
-<p>$r$ is the <strong>average of the products of the two variables</strong>, when both variables are measured in standard units.</p>
-<p>Here are the steps in the calculation. We will apply the steps to a simple table of values of <strong>x</strong> and <strong>y</strong>.</p>
-</div>
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-<div class=" highlight hl-ipython3"><pre><span></span><span class="n">x</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">7</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
-<span class="n">y</span> <span class="o">=</span> <span class="n">make_array</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">7</span><span class="p">)</span>
-<span class="n">t</span> <span class="o">=</span> <span class="n">Table</span><span class="p">()</span><span class="o">.</span><span class="n">with_columns</span><span class="p">(</span>
-        <span class="s1">&#39;x&#39;</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span>
-        <span class="s1">&#39;y&#39;</span><span class="p">,</span> <span class="n">y</span>
-    <span class="p">)</span>
-<span class="n">t</span>
-</pre></div>
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-<table border="1" class="dataframe">
-    <thead>
-        <tr>
-            <th>x</th> <th>y</th>
-        </tr>
-    </thead>
-    <tbody>
-        <tr>
-            <td>1   </td> <td>2   </td>
-        </tr>
-        <tr>
-            <td>2   </td> <td>3   </td>
-        </tr>
-        <tr>
-            <td>3   </td> <td>1   </td>
-        </tr>
-        <tr>
-            <td>4   </td> <td>5   </td>
-        </tr>
-        <tr>
-            <td>5   </td> <td>2   </td>
-        </tr>
-        <tr>
-            <td>6   </td> <td>7   </td>
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-<p>Based on the scatter diagram, we expect that $r$ will be positive but not equal to 1.</p>
-</div>
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-<div class=" highlight hl-ipython3"><pre><span></span><span class="n">nbi</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">column</span><span class="p">(</span><span class="mi">0</span><span class="p">),</span> <span class="n">t</span><span class="o">.</span><span class="n">column</span><span class="p">(</span><span class="mi">1</span><span class="p">),</span> <span class="n">options</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;aspect_ratio&#39;</span><span class="p">:</span> <span class="mi">1</span><span class="p">})</span>
-</pre></div>
-    </div>
-</div>
-</div>
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-<p><strong>Step 1.</strong> Convert each variable to standard units.</p>
-</div>
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-<div class=" highlight hl-ipython3"><pre><span></span><span class="k">def</span> <span class="nf">standard_units</span><span class="p">(</span><span class="n">nums</span><span class="p">):</span>
-    <span class="k">return</span> <span class="p">(</span><span class="n">nums</span> <span class="o">-</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">nums</span><span class="p">))</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">std</span><span class="p">(</span><span class="n">nums</span><span class="p">)</span>
-</pre></div>
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-<div class=" highlight hl-ipython3"><pre><span></span><span class="n">t_su</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="n">with_columns</span><span class="p">(</span>
-        <span class="s1">&#39;x (standard units)&#39;</span><span class="p">,</span> <span class="n">standard_units</span><span class="p">(</span><span class="n">x</span><span class="p">),</span>
-        <span class="s1">&#39;y (standard units)&#39;</span><span class="p">,</span> <span class="n">standard_units</span><span class="p">(</span><span class="n">y</span><span class="p">)</span>
-    <span class="p">)</span>
-<span class="n">t_su</span>
-</pre></div>
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-<table border="1" class="dataframe">
-    <thead>
-        <tr>
-            <th>x</th> <th>y</th> <th>x (standard units)</th> <th>y (standard units)</th>
-        </tr>
-    </thead>
-    <tbody>
-        <tr>
-            <td>1   </td> <td>2   </td> <td>-1.46385          </td> <td>-0.648886         </td>
-        </tr>
-        <tr>
-            <td>2   </td> <td>3   </td> <td>-0.87831          </td> <td>-0.162221         </td>
-        </tr>
-        <tr>
-            <td>3   </td> <td>1   </td> <td>-0.29277          </td> <td>-1.13555          </td>
-        </tr>
-        <tr>
-            <td>4   </td> <td>5   </td> <td>0.29277           </td> <td>0.811107          </td>
-        </tr>
-        <tr>
-            <td>5   </td> <td>2   </td> <td>0.87831           </td> <td>-0.648886         </td>
-        </tr>
-        <tr>
-            <td>6   </td> <td>7   </td> <td>1.46385           </td> <td>1.78444           </td>
-        </tr>
-    </tbody>
-</table>
-</div>
-</div>
-</div>
-</div>
-  </div>
-<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
-<div class="text_cell_render border-box-sizing rendered_html">
-<p><strong>Step 2.</strong> Multiply each pair of standard units.</p>
-</div>
-</div>
-</div>
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-<div class=" highlight hl-ipython3"><pre><span></span><span class="n">t_product</span> <span class="o">=</span> <span class="n">t_su</span><span class="o">.</span><span class="n">with_column</span><span class="p">(</span><span class="s1">&#39;product of standard units&#39;</span><span class="p">,</span> <span class="n">t_su</span><span class="o">.</span><span class="n">column</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span> <span class="o">*</span> <span class="n">t_su</span><span class="o">.</span><span class="n">column</span><span class="p">(</span><span class="mi">3</span><span class="p">))</span>
-<span class="n">t_product</span>
-</pre></div>
-    </div>
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-<table border="1" class="dataframe">
-    <thead>
-        <tr>
-            <th>x</th> <th>y</th> <th>x (standard units)</th> <th>y (standard units)</th> <th>product of standard units</th>
-        </tr>
-    </thead>
-    <tbody>
-        <tr>
-            <td>1   </td> <td>2   </td> <td>-1.46385          </td> <td>-0.648886         </td> <td>0.949871                 </td>
-        </tr>
-        <tr>
-            <td>2   </td> <td>3   </td> <td>-0.87831          </td> <td>-0.162221         </td> <td>0.142481                 </td>
-        </tr>
-        <tr>
-            <td>3   </td> <td>1   </td> <td>-0.29277          </td> <td>-1.13555          </td> <td>0.332455                 </td>
-        </tr>
-        <tr>
-            <td>4   </td> <td>5   </td> <td>0.29277           </td> <td>0.811107          </td> <td>0.237468                 </td>
-        </tr>
-        <tr>
-            <td>5   </td> <td>2   </td> <td>0.87831           </td> <td>-0.648886         </td> <td>-0.569923                </td>
-        </tr>
-        <tr>
-            <td>6   </td> <td>7   </td> <td>1.46385           </td> <td>1.78444           </td> <td>2.61215                  </td>
-        </tr>
-    </tbody>
-</table>
-</div>
-</div>
-</div>
-</div>
-  </div>
-<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
-<div class="text_cell_render border-box-sizing rendered_html">
-<p><strong>Step 3.</strong> $r$ is the average of the products computed in Step 2.</p>
-</div>
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-<div class=" highlight hl-ipython3"><pre><span></span><span class="c1"># r is the average of the products of standard units</span>
-<span class="n">r</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">t_product</span><span class="o">.</span><span class="n">column</span><span class="p">(</span><span class="mi">4</span><span class="p">))</span>
-<span class="n">r</span>
-</pre></div>
-    </div>
-</div>
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-<pre>0.6174163971897709</pre>
-</div>
-</div>
-</div>
-</div>
-  </div>
-<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
-<div class="text_cell_render border-box-sizing rendered_html">
-<p>As expected, $r$ is positive but not equal to 1.</p>
-</div>
-</div>
-</div>
-<div class="cell border-box-sizing text_cell rendered"><div class="inner_cell">
-<div class="text_cell_render border-box-sizing rendered_html">
-<h4 id="Properties-of-$r$">Properties of $r$<a class="anchor-link" href="#Properties-of-$r$">&#182;</a></h4><p>The calculation shows that:</p>
-<ul>
-<li>$r$ is a pure number. It has no units. This is because $r$ is based on standard units.</li>
-<li>$r$ is unaffected by changing the units on either axis. This too is because $r$ is based on standard units.</li>
-<li>$r$ is unaffected by switching the axes. Algebraically, this is because the product of standard units does not depend on which variable is called <strong>x</strong> and which <strong>y</strong>. Geometrically, switching axes reflects the scatter plot about the line <strong>y = x</strong>, but does not change the amount of clustering nor the sign of the association.</li>
-</ul>
-</div>
-</div>
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-<div class=" highlight hl-ipython3"><pre><span></span><span class="n">nbi</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">column</span><span class="p">(</span><span class="mi">1</span><span class="p">),</span> <span class="n">t</span><span class="o">.</span><span class="n">column</span><span class="p">(</span><span class="mi">0</span><span class="p">),</span> <span class="n">options</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;aspect_ratio&#39;</span><span class="p">:</span> <span class="mi">1</span><span class="p">})</span>
-</pre></div>
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-<h4 id="The-correlation-function">The correlation function<a class="anchor-link" href="#The-correlation-function">&#182;</a></h4><p>We are going to be calculating correlations repeatedly, so it will help to define a function that computes it by performing all the steps described above. Let's define a function <code>correlation</code> that takes a table and the labels of two columns in the table. The function returns $r$, the mean of the products of those column values in standard units.</p>
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-<div class=" highlight hl-ipython3"><pre><span></span><span class="k">def</span> <span class="nf">correlation</span><span class="p">(</span><span class="n">t</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
-    <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">standard_units</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">column</span><span class="p">(</span><span class="n">x</span><span class="p">))</span><span class="o">*</span><span class="n">standard_units</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">column</span><span class="p">(</span><span class="n">y</span><span class="p">)))</span>
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-<div class=" highlight hl-ipython3"><pre><span></span><span class="n">interact</span><span class="p">(</span><span class="n">correlation</span><span class="p">,</span> <span class="n">t</span><span class="o">=</span><span class="n">fixed</span><span class="p">(</span><span class="n">t</span><span class="p">),</span>
-         <span class="n">x</span><span class="o">=</span><span class="n">widgets</span><span class="o">.</span><span class="n">ToggleButtons</span><span class="p">(</span><span class="n">options</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;x&#39;</span><span class="p">,</span> <span class="s1">&#39;y&#39;</span><span class="p">],</span> <span class="n">description</span><span class="o">=</span><span class="s1">&#39;x-axis&#39;</span><span class="p">),</span>
-         <span class="n">y</span><span class="o">=</span><span class="n">widgets</span><span class="o">.</span><span class="n">ToggleButtons</span><span class="p">(</span><span class="n">options</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;x&#39;</span><span class="p">,</span> <span class="s1">&#39;y&#39;</span><span class="p">],</span> <span class="n">description</span><span class="o">=</span><span class="s1">&#39;y-axis&#39;</span><span class="p">))</span>
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-<pre>&lt;function __main__.correlation(t, x, y)&gt;</pre>
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-<p>Let's call the function on the <code>x</code> and <code>y</code> columns of <code>t</code>. The function returns the same answer to the correlation between $x$ and $y$ as we got by direct application of the formula for $r$.</p>
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-<div class=" highlight hl-ipython3"><pre><span></span><span class="n">correlation</span><span class="p">(</span><span class="n">t</span><span class="p">,</span> <span class="s1">&#39;x&#39;</span><span class="p">,</span> <span class="s1">&#39;y&#39;</span><span class="p">)</span>
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-<pre>0.6174163971897709</pre>
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-<p>As we noticed, the order in which the variables are specified doesn't matter.</p>
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-<div class=" highlight hl-ipython3"><pre><span></span><span class="n">correlation</span><span class="p">(</span><span class="n">t</span><span class="p">,</span> <span class="s1">&#39;y&#39;</span><span class="p">,</span> <span class="s1">&#39;x&#39;</span><span class="p">)</span>
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-<pre>0.6174163971897709</pre>
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-<p>Calling <code>correlation</code> on columns of the table <code>suv</code> gives us the correlation between price and mileage as well as the correlation between price and acceleration.</p>
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-       <span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="s1">&#39;class&#39;</span><span class="p">,</span> <span class="s1">&#39;SUV&#39;</span><span class="p">))</span>
-<span class="n">interact</span><span class="p">(</span><span class="n">correlation</span><span class="p">,</span> <span class="n">t</span><span class="o">=</span><span class="n">fixed</span><span class="p">(</span><span class="n">suv</span><span class="p">),</span>
-         <span class="n">x</span><span class="o">=</span><span class="n">widgets</span><span class="o">.</span><span class="n">ToggleButtons</span><span class="p">(</span><span class="n">options</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;mpg&#39;</span><span class="p">,</span> <span class="s1">&#39;msrp&#39;</span><span class="p">,</span> <span class="s1">&#39;acceleration&#39;</span><span class="p">],</span>
-                                 <span class="n">description</span><span class="o">=</span><span class="s1">&#39;x-axis&#39;</span><span class="p">),</span>
-         <span class="n">y</span><span class="o">=</span><span class="n">widgets</span><span class="o">.</span><span class="n">ToggleButtons</span><span class="p">(</span><span class="n">options</span><span class="o">=</span><span class="p">[</span><span class="s1">&#39;mpg&#39;</span><span class="p">,</span> <span class="s1">&#39;msrp&#39;</span><span class="p">,</span> <span class="s1">&#39;acceleration&#39;</span><span class="p">],</span>
-                                 <span class="n">description</span><span class="o">=</span><span class="s1">&#39;y-axis&#39;</span><span class="p">))</span>
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-<pre>&lt;function __main__.correlation(t, x, y)&gt;</pre>
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-<div class=" highlight hl-ipython3"><pre><span></span><span class="n">correlation</span><span class="p">(</span><span class="n">suv</span><span class="p">,</span> <span class="s1">&#39;mpg&#39;</span><span class="p">,</span> <span class="s1">&#39;msrp&#39;</span><span class="p">)</span>
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-<pre>-0.6667143635709919</pre>
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-<div class=" highlight hl-ipython3"><pre><span></span><span class="n">correlation</span><span class="p">(</span><span class="n">suv</span><span class="p">,</span> <span class="s1">&#39;acceleration&#39;</span><span class="p">,</span> <span class="s1">&#39;msrp&#39;</span><span class="p">)</span>
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-<pre>0.48699799279959155</pre>
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-<p>These values confirm what we had observed:</p>
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-<li>There is a negative association between price and efficiency, whereas the association between price and acceleration is positive.</li>
-<li>The linear relation between price and acceleration is a little weaker (correlation about 0.5) than between price and mileage (correlation about -0.67). </li>
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-<p>Correlation is a simple and powerful concept, but it is sometimes misused. Before using $r$, it is important to be aware of what correlation does and does not measure.</p>
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