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Built site for AMR@3.0.0.9029: c7b2acb
This commit is contained in:
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@@ -7,7 +7,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9021</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9029</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@@ -110,30 +110,30 @@
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="va">sir</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] R R I R I I S R S I</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I I R I R S S S I S</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.1618950 1.1618950 -0.7745967 1.1618950 -0.7745967 -0.7745967</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.7745967 1.1618950 -0.7745967 -0.7745967</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.4743416 -0.4743416 1.8973666 -0.4743416 1.8973666 -0.4743416</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4743416 -0.4743416 -0.4743416 -0.4743416</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">mic</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="va">mic</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'mic'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.032 0.5 1 >=8 4 0.016 >=8 1 0.004 0.008</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.004 2 0.002 0.0001 0.004 0.002 >=4 0.0002 0.032 0.004 </span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.7311752 0.2104422 0.4478776 1.1601837 0.9227483 -0.9686106</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.1601837 0.4478776 -1.4434813 -1.2060459</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.2047915 1.5799751 -0.4038557 -1.2641969 -0.2047915 -0.4038557</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.7790393 -1.0651327 0.3924011 -0.2047915</span>
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<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
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<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.7311752 0.2104422 0.4478776 1.1601837 0.9227483 -0.9686106</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.1601837 0.4478776 -1.4434813 -1.2060459</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.2047915 1.5799751 -0.4038557 -1.2641969 -0.2047915 -0.4038557</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.7790393 -1.0651327 0.3924011 -0.2047915</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">disk</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="va">disk</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 50 49 38 33 31 17 42 43 46 37</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 43 12 28 32 22 31 35 25 43 35</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.15131286 1.05032051 -0.06059541 -0.56555720 -0.76754191 -2.18143490</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.34337401 0.44436637 0.74734344 -0.16158777</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.30998909 -1.96498364 -0.27467513 0.14790199 -0.90854082 0.04225771</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.46483484 -0.59160798 1.30998909 0.46483484</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">y</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
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<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
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@@ -144,35 +144,35 @@
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="va">y</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A I 27 >=2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 28 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 33 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 32 1 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 25 0.5 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 19 0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 23 0.5 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 27 0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 29 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 32 0.5 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A S 31 2 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 27 <=1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 25 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 25 <=1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 31 <=1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 32 <=1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 29 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 18 <=1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 28 <=1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 17 <=1 2</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> and "tobr"</span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.08471751 -0.21572693 0.55391610 0.98093500 -0.26046456 -1.08721162</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.37467261 -0.14625651 -0.15862291 0.62338653</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.90606144 -0.03989270 0.66241774 -0.09230226 -0.32300020 0.19914999</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.09893189 -0.70734036 -0.22925499 -0.47477055</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">y</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span></span>
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<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 19 0.5 8 -0.8163565</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 27 0.5 8 -0.8163565</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 28 1 8 -0.1012596</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 33 1 8 -0.1012596</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 29 1 8 -0.1012596</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 25 0.5 16 0.1518893</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 23 0.5 16 0.1518893</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 32 0.5 16 0.1518893</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A I 27 >=2 8 0.6138374</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 32 1 16 0.8669863</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 25 <=1 2 -0.7848712</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 31 <=1 2 -0.7848712</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 17 <=1 2 -0.7848712</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 18 <=1 4 -0.3105295</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 28 <=1 4 -0.3105295</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 27 <=1 8 0.1638121</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 32 <=1 8 0.1638121</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 29 2 2 0.2502272</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 25 2 4 0.7245688</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A S 31 2 >=16 1.6732521</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span> <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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@@ -185,16 +185,16 @@
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> and "tobr"</span></span>
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<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C R 33 1 8 0.55391610 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 J R 32 0.5 16 0.62338653 0.06947042</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 D R 32 1 16 0.98093500 0.42701889</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A I 27 >=2 8 0.08471751 0.46919859</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 H R 27 0.5 8 -0.14625651 0.70017262</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I S 29 1 8 -0.15862291 0.71253901</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B S 28 1 8 -0.21572693 0.76964304</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 E I 25 0.5 16 -0.26046456 0.81438066</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 G S 23 0.5 16 -0.37467261 0.92858871</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 F I 19 0.5 8 -1.08721162 1.64112773</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C R 25 2 4 0.66241774 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 A S 31 2 >=16 0.90606144 0.2436437</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 F S 32 <=1 8 0.19914999 0.4632678</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G I 29 2 2 0.09893189 0.5634858</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 B S 27 <=1 8 -0.03989270 0.7023104</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 D R 25 <=1 2 -0.09230226 0.7547200</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 I S 28 <=1 4 -0.22925499 0.8916727</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 E I 31 <=1 2 -0.32300020 0.9854179</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J R 17 <=1 2 -0.47477055 1.1371883</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 H S 18 <=1 4 -0.70734036 1.3697581</span>
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
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<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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