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Built site for AMR: 1.8.2.9095@24b1202
This commit is contained in:
github-actions
@@ -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="">1.8.2.9094</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9095</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] S S I R S I R S S R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S S S I I R S S I 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 1.449138 -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 1.449138</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.3162278 -0.3162278 -0.3162278 -0.3162278 -0.3162278 2.8460499</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.3162278 -0.3162278 -0.3162278 -0.3162278</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] 0.125 2 8 0.5 0.002 4 0.025 4 32 128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.25 16 0.01 0.002 2 0.002 0.025 >=256 16 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] -0.6558590 0.1714027 0.5850335 -0.2422282 -1.8896751 0.3782181</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.1360695 0.3782181 0.9986643 1.4122951</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.1484568 0.8300945 -0.9058320 -1.2845196 0.3408189 -1.2845196</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.6902363 1.4824620 0.8300945 0.8300945</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] -0.6558590 0.1714027 0.5850335 -0.2422282 -1.8896751 0.3782181</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.1360695 0.3782181 0.9986643 1.4122951</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.1484568 0.8300945 -0.9058320 -1.2845196 0.3408189 -1.2845196</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.6902363 1.4824620 0.8300945 0.8300945</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] 47 10 18 45 33 35 18 41 45 47</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 44 8 43 18 44 10 32 16 14 6</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] 0.94791030 -1.72939361 -1.15051709 0.80319117 -0.06512361 0.07959552</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.15051709 0.51375291 0.80319117 0.94791030</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.3116316 -0.9917215 1.2476496 -0.3519012 1.3116316 -0.8637574</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.5438473 -0.4798652 -0.6078293 -1.1196855</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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@@ -224,36 +224,36 @@
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<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
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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 17 0.25 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 31 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 24 >=4 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 24 0.25 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 31 >=4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 19 0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 27 0.5 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 31 0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 18 0.25 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 31 >=4 2</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 R 25 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 28 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 27 16 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 25 1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 29 <=0.25 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 30 1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 31 4 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 31 16 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 19 1 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 19 8 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> 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] -0.89400136 0.13637933 0.51178793 -0.33268016 0.81891467 -0.78894215</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.20168990 -0.01042573 -0.59026102 0.94753861</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.4205821 0.1957997 0.4383306 -0.1767834 -0.5439764 -0.4135734</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.4143153 0.6629379 -0.6880658 -0.3095667</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> 9 I R 18 0.25 0.25 -1.27088082</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A S 17 0.25 1 -0.75638506</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F S 19 0.5 0.5 -0.72002283</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 24 0.25 4 -0.24188931</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 31 0.5 2 -0.20552708</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 31 1 2 0.08808303</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 31 >=4 1 0.41805537</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 27 0.5 16 0.56621656</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J R 31 >=4 2 0.67530325</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 24 >=4 16 1.44704689</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> 9 I R 19 1 <=0.25 -1.2696534</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 29 <=0.25 1 -1.0694127</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 25 1 0.5 -0.9209105</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 30 1 0.5 -0.9209105</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A R 25 4 2 0.2738205</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 28 8 2 0.5224431</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 19 8 2 0.5224431</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G I 31 4 >=4 0.6225634</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C I 27 16 >=4 1.1198086</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H I 31 16 >=4 1.1198086</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 24 >=4 16 0.51178793 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 E R 31 >=4 1 0.81891467 0.3071267</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 G S 27 0.5 16 0.20168990 0.3100980</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B I 31 1 2 0.13637933 0.3754086</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 J R 31 >=4 2 0.94753861 0.4357507</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H I 31 0.5 2 -0.01042573 0.5222137</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D S 24 0.25 4 -0.33268016 0.8444681</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 I R 18 0.25 0.25 -0.59026102 1.1020490</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 F S 19 0.5 0.5 -0.78894215 1.3007301</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A S 17 0.25 1 -0.89400136 1.4057893</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 27 16 >=4 0.4383306 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 A R 25 4 2 0.4205821 0.01774851</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 G I 31 4 >=4 0.4143153 0.02401530</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 H I 31 16 >=4 0.6629379 0.22460728</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 B S 28 8 2 0.1957997 0.24253093</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 D R 25 1 0.5 -0.1767834 0.61511400</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 J I 19 8 2 -0.3095667 0.74789731</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 F I 30 1 0.5 -0.4135734 0.85190407</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E S 29 <=0.25 1 -0.5439764 0.98230701</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 I R 19 1 <=0.25 -0.6880658 1.12639638</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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