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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="">3.0.1.9026</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9030</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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@@ -110,31 +110,31 @@
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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 I R I I S R S I I</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S R S R I I R R R 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] 1.449138 -0.621059 1.449138 -0.621059 -0.621059 -0.621059 1.449138</span>
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<span class="r-out co"><span class="r-pr">#></span> [8] -0.621059 -0.621059 -0.621059</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.9486833 0.9486833 -0.9486833 0.9486833 -0.9486833 -0.9486833</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.9486833 0.9486833 0.9486833 -0.9486833</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] 0.25 0.5 8 2 0.004 4 1 0.001 </span>
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<span class="r-out co"><span class="r-pr">#></span> [9] 0.004 <=0.0005</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 <=0.0001 0.25 0.0005 0.001 0.0002 8 <=0.0001</span>
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<span class="r-out co"><span class="r-pr">#></span> [9] <=0.0001 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] 0.2626139 0.4520471 1.2097801 0.8309136 -0.8675039 1.0203468</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.6414804 -1.2463704 -0.8675039 -1.4358036</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.18999891 -0.86809178 1.02250714 -0.47918793 -0.31169616 -0.70060001</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.85996599 -0.86809178 -0.86809178 0.02328738</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] 0.2626139 0.4520471 1.2097801 0.8309136 -0.8675039 1.0203468</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.6414804 -1.2463704 -0.8675039 -1.4358036</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.18999891 -0.86809178 1.02250714 -0.47918793 -0.31169616 -0.70060001</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.85996599 -0.86809178 -0.86809178 0.02328738</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] 49 38 33 31 17 42 43 46 37 46</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 20 45 31 26 23 38 44 41 20 49</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] 1.14152462 -0.02113934 -0.54962296 -0.76101641 -2.24077054 0.40164755</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.50734427 0.82443445 -0.12683607 0.82443445</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.2414143 1.0239402 -0.2446583 -0.6977292 -0.9695717 0.3896410</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.9333261 0.6614835 -1.2414143 1.3863970</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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@@ -145,35 +145,35 @@
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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 S 28 >=2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 33 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 32 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 25 1 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 19 0.5 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 23 0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 27 0.5 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 29 0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 32 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 R 33 16 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 32 <=8 32</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 27 16 32</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 33 <=8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 22 <=8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 32 <=8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 31 16 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 31 <=8 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 28 16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 22 16 4</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] 0.06974787 0.45859464 0.40418392 0.03309016 -0.65092262 -0.91740267</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.25870477 -0.59093836 0.40418392 0.53075837</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.52677313 0.16501937 0.34372779 -0.05155946 -0.97765805 0.26901032</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.30452889 -0.58337098 0.36899264 -0.36546366</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 S 23 0.5 8 -0.8163565</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 29 0.5 8 -0.8163565</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B R 33 1 8 -0.1012596</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 32 1 8 -0.1012596</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 32 1 8 -0.1012596</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 19 0.5 16 0.1518893</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 27 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 S 28 >=2 8 0.6138374</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 25 1 16 0.8669863</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 31 <=8 <=1 -1.0808937</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 22 <=8 2 -0.8051882</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 32 <=8 4 -0.5294827</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D I 33 <=8 8 -0.2537773</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A R 33 16 <=1 -0.1322104</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 28 16 2 0.1434951</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 32 <=8 32 0.2976337</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 22 16 4 0.4192006</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 31 16 8 0.6949060</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 27 16 32 1.2463170</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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@@ -186,16 +186,16 @@
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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 32 1 8 0.40418392 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 I R 32 1 8 0.40418392 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 B R 33 1 8 0.45859464 0.05441072</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 J R 32 0.5 16 0.53075837 0.12657445</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 G R 27 0.5 16 0.25870477 0.14547915</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A S 28 >=2 8 0.06974787 0.33443605</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D I 25 1 16 0.03309016 0.37109376</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 29 0.5 8 -0.59093836 0.99512228</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E I 19 0.5 16 -0.65092262 1.05510655</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 F S 23 0.5 8 -0.91740267 1.32158659</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 C S 27 16 32 0.34372779 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 I R 28 16 2 0.36899264 0.02526485</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 G S 31 16 8 0.30452889 0.03919890</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F R 32 <=8 4 0.26901032 0.07471748</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 B S 32 <=8 32 0.16501937 0.17870842</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A R 33 16 <=1 0.52677313 0.18304534</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D I 33 <=8 8 -0.05155946 0.39528726</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 J S 22 16 4 -0.36546366 0.70919145</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 H I 31 <=8 <=1 -0.58337098 0.92709877</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 E I 22 <=8 2 -0.97765805 1.32138584</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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Reference in New Issue
Block a user