deploy: 9643b66

lisds · Jun 3, 2024 · 01d2dd0 · 01d2dd0
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diff --git a/_images/fe844dc70fc708e5f782411a9df6bb5743d594203159bcf43dd3b7b67899d481.png b/_images/fe844dc70fc708e5f782411a9df6bb5743d594203159bcf43dd3b7b67899d481.png
diff --git a/_sources/permutation/permutation_pairs.Rmd b/_sources/permutation/permutation_pairs.Rmd
@@ -119,18 +119,30 @@ mosq_counts = beer_afters[['no_odour', 'volunt_odour']]
 mosq_counts.head()
 ```
 
-And do our planned subtraction of the control `no_odour` numbers from the experimental `volunt_odour` numbers:
+And do our planned subtraction of the control `no_odour` numbers from the experimental `volunt_odour` numbers.
 
 ```{python}
-mosq_counts['person_minus_empty'] = (mosq_counts['volunt_odour'] -
-                                     mosq_counts['no_odour'])
+# Transfer to arrays for simplicity.
+empty = np.array(mosq_counts['no_odour'])
+person = np.array(mosq_counts['volunt_odour'])
+```
+
+```{python}
+actual_diffs = person - empty
+actual_diffs
+```
+
+Here we show the result using Pandas, of which more soon in the course:
+
+```{python}
+mosq_counts['person_minus_empty'] = person - empty
 mosq_counts.head()
 ```
 
 If our hypothesis is correct, we expect this difference (person counts minus control counts) to be positive, on average.  Let's see what this average difference was for our sample:
 
 ```{python}
-actual_mean_diff = mosq_counts['person_minus_empty'].mean()
+actual_mean_diff = np.mean(actual_diffs)
 actual_mean_diff
 ```
 
@@ -154,7 +166,11 @@ scores.  Then we would recalculate the mean difference, and this mean difference
 
 We could do this operation, of going through each row, and randomly flipping the `volunt_odour` and `no_odour` values, but we can also simplify our task with a tiny bit of algebra.
 
-Let's say we have the subtraction between any two values $x$ and $y$: $d = x - y$, but we want the subtraction the other way round: $y - x$.  But:
+Let's say we have the subtraction between any two values $x$ and $y$: $d = x - y$, and we want the subtraction the other way round: $y - x$.  But:
+
+$$
+d = x - y
+$$
 
 $$
 y - x = -(y - x) = -d
@@ -175,10 +191,10 @@ rand_signs
 
 The values of -1 represent rows for which we are flipping the pairs, and values of 1 correspond to pairs we have left in the original order.
 
-Here were the original differences:
+Here we recalculate the differences, as we did above:
 
 ```{python}
-actual_diffs = np.array(mosq_counts['person_minus_empty'])
+actual_diffs = person - empty
 actual_diffs
 ```
 
@@ -237,7 +253,7 @@ results[:10]
 plt.hist(results, bins=50)
 plt.title('Sampling distribution of mean of differences')
 plt.axvline(actual_mean_diff, color='red', label='Actual value')
-plt.legend()
+plt.legend();
 ```
 
 Finally we ask how unusual the actual value is in the sampling distribution from the null world:

diff --git a/arrays/boolean_arrays.html b/arrays/boolean_arrays.html
@@ -658,7 +658,7 @@ <h1>Boolean arrays<a class="headerlink" href="#boolean-arrays" title="Link to th
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+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([1, 1, 1, 1])
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+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([False,  True, False, False,  True])
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diff --git a/arrays/leaping_ahead.html b/arrays/leaping_ahead.html
@@ -771,7 +771,7 @@ <h1>Leaping ahead<a class="headerlink" href="#leaping-ahead" title="Link to this
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+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([1., 3., 3., 2., 1., 3., 2., 1., 2., 3.])
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@@ -808,7 +808,7 @@ <h1>Leaping ahead<a class="headerlink" href="#leaping-ahead" title="Link to this
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+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>2451
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@@ -823,7 +823,7 @@ <h1>Leaping ahead<a class="headerlink" href="#leaping-ahead" title="Link to this
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-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0.2541
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0.2451
 </pre></div>
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@@ -857,7 +857,7 @@ <h2>The whole thing<a class="headerlink" href="#the-whole-thing" title="Link to
 </div>
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 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0.2568
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0.2515
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diff --git a/arrays/rng_choice.html b/arrays/rng_choice.html
@@ -673,7 +673,7 @@ <h1>Random choice<a class="headerlink" href="#random-choice" title="Link to this
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>1
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0
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@@ -693,7 +693,7 @@ <h1>Random choice<a class="headerlink" href="#random-choice" title="Link to this
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+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>1
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-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1])
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0])
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@@ -766,7 +766,7 @@ <h2>Multiple choices with <code class="docutils literal notranslate"><span class
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-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([0, 0, 1, 1])
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([0, 1, 1, 0])
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@@ -783,7 +783,7 @@ <h2>Multiple choices with <code class="docutils literal notranslate"><span class
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-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([1, 0, 1, 1])
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-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([9, 1, 3])
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([9, 7, 0])
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-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([7, 8, 4])
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-       9, 9, 1, 6, 4, 9, 9, 8, 1, 1, 9, 4, 4, 8, 7, 1, 6, 5, 6, 5, 4, 2,
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-       3, 8, 0, 4, 7, 3, 6, 3, 2, 2, 0, 1, 3, 9, 0, 2, 2, 7, 6, 6, 2, 2,
-       9, 0, 3, 7, 0, 6, 3, 2, 8, 2, 0, 9])
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>array([8, 8, 2, 8, 1, 0, 5, 9, 3, 9, 7, 1, 7, 4, 9, 1, 5, 4, 5, 1, 9, 1,
+       9, 5, 5, 0, 8, 7, 3, 6, 0, 9, 1, 1, 9, 7, 7, 8, 4, 2, 1, 6, 9, 8,
+       6, 6, 8, 4, 3, 5, 6, 1, 1, 9, 6, 5, 4, 4, 2, 5, 2, 9, 6, 5, 3, 8,
+       0, 7, 3, 4, 8, 1, 6, 5, 2, 3, 8, 2, 8, 4, 1, 7, 1, 5, 2, 6, 3, 0,
+       1, 6, 1, 4, 4, 2, 4, 8, 4, 9, 8, 5])
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 </div>

diff --git a/classification/Accuracy_of_the_Classifier.html b/classification/Accuracy_of_the_Classifier.html
@@ -786,7 +786,7 @@ <h2>Measuring the Accuracy of Our Wine Classifier<a class="headerlink" href="#me
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-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0.8876404494382022
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0.9550561797752809
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@@ -943,7 +943,7 @@ <h2>Breast Cancer Diagnosis<a class="headerlink" href="#breast-cancer-diagnosis"
 <p>Oops.  That plot is utterly misleading, because there are a bunch of points that have identical values for both the x- and y-coordinates.  To make it easier to see all the data points, I’m going to add a little bit of random jitter to the x- and y-values.  Here’s how that looks:</p>
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-<img alt="../_images/4a93c97034f3e5462fc0ad695161f0f1e4e9f842da2e37e8cc72dfa46dd54f52.png" src="../_images/4a93c97034f3e5462fc0ad695161f0f1e4e9f842da2e37e8cc72dfa46dd54f52.png" />
+<img alt="../_images/77ee22559c2ee08fc3d10834e49a1532ea8c99b1920134039eb477974846c85d.png" src="../_images/77ee22559c2ee08fc3d10834e49a1532ea8c99b1920134039eb477974846c85d.png" />
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 <p>For instance, you can see there are lots of samples with chromatin = 2 and epithelial cell size = 2; all non-cancerous.</p>
@@ -967,7 +967,7 @@ <h2>Breast Cancer Diagnosis<a class="headerlink" href="#breast-cancer-diagnosis"
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-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0.9589442815249267
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>0.9736070381231672
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