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Built site for AMR: 1.8.2.9091@33f269e
This commit is contained in:
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@ -10,7 +10,7 @@
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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="">1.8.2.9090</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9091</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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@ -191,30 +191,30 @@
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">rsi</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_rsi</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">rsi</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'rsi'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I S I I S I R R S R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] I S I S I R R S S I</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">rsi</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.621059 -0.621059 -0.621059 -0.621059 -0.621059 -0.621059 1.449138</span>
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<span class="r-out co"><span class="r-pr">#></span> [8] 1.449138 -0.621059 1.449138</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.4743416 -0.4743416 -0.4743416 -0.4743416 -0.4743416 1.8973666</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.8973666 -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] 1 0.025 0.002 0.5 0.002 64 64 16 32 256 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 0.125 0.005 64 2 0.5 0.002 1 >=256 16 </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] -0.07454929 -0.91041921 -1.48272867 -0.23161077 -1.48272867 0.86781961</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.86781961 0.55369665 0.71075813 1.18194258</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.13590568 -0.50369749 -1.35768361 1.15136563 0.23188612 -0.13590568</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.60078077 0.04799022 1.51915743 0.78357383</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] -0.07454929 -0.91041921 -1.48272867 -0.23161077 -1.48272867 0.86781961</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.86781961 0.55369665 0.71075813 1.18194258</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.13590568 -0.50369749 -1.35768361 1.15136563 0.23188612 -0.13590568</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.60078077 0.04799022 1.51915743 0.78357383</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] 48 33 18 35 49 8 14 36 49 45</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 19 35 29 49 16 45 40 46 43 44</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] 0.94868330 -0.03271322 -1.01410973 0.09813965 1.01410973 -1.66837408</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.27581547 0.16356609 1.01410973 0.75240400</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.5151410 -0.1377401 -0.6542654 1.0674857 -1.7734036 0.7231355</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.2926977 0.8092230 0.5509604 0.6370479</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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@ -225,35 +225,35 @@
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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 19 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 20 <=2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 29 <=2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 23 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 29 4 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 30 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 19 16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 17 <=2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 29 16 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 27 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A I 22 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 18 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 29 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 27 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 18 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 28 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 29 2 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 24 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 30 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 19 0.5 1</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> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.61849512 -0.37440074 0.06535968 -0.22102136 0.28096952 0.12101452</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.01474925 0.07193952 0.67866446 -0.01877971</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.4635438 -0.2522842 0.6793050 -0.0301707 -0.1458327 0.2647728</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.7200702 -0.5349771 0.5561661 -0.7935056</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</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> 1 A I 19 8 0.5 -0.49165184</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 20 <=2 >=4 -0.10118760</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 29 <=2 >=4 -0.10118760</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 17 <=2 >=4 -0.10118760</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 23 4 2 -0.08760245</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 30 4 2 -0.08760245</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 27 8 1 -0.07401730</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 29 16 0.5 -0.06043216</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 29 4 >=4 0.33003208</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 19 16 2 0.77483691</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 18 0.5 1 -0.79141880</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 28 0.5 1 -0.79141880</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 24 0.5 1 -0.79141880</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 19 0.5 1 -0.79141880</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A I 22 1 1 -0.44172950</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 27 2 1 -0.09204019</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 18 8 1 0.60733841</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 30 2 4 0.77039917</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 29 4 4 1.12008847</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 29 2 >=8 1.20161885</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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@ -265,17 +265,17 @@
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "tobr"</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 I 29 <=2 >=4 0.06535968 0.000000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H R 17 <=2 >=4 0.07193952 0.006579847</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 G S 19 16 2 0.01474925 0.050610425</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F S 30 4 2 0.12101452 0.055654841</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 J S 27 8 1 -0.01877971 0.084139390</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E S 29 4 >=4 0.28096952 0.215609840</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D S 23 4 2 -0.22102136 0.286381034</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 B I 20 <=2 >=4 -0.37440074 0.439760411</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 29 16 0.5 0.67866446 0.613304780</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A I 19 8 0.5 -0.61849512 0.683854800</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 S 29 4 4 0.6793050 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G I 29 2 >=8 0.7200702 0.04076519</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I S 30 2 4 0.5561661 0.12313895</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F R 28 0.5 1 0.2647728 0.41453227</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D I 27 2 1 -0.0301707 0.70947573</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E I 18 8 1 -0.1458327 0.82513769</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B R 18 0.5 1 -0.2522842 0.93158924</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 A I 22 1 1 -0.4635438 1.14284886</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 H I 24 0.5 1 -0.5349771 1.21428212</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 19 0.5 1 -0.7935056 1.47281060</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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