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Built site for AMR: 1.8.2.9052@05d536e

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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9051</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9052</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -200,11 +200,10 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</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>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 16 0.0625 1 &lt;=0.002 32 0.5 0.025 256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0625 0.0625 1 0.025 8 32 0.5 &gt;=128 0.002 0.0625</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.64690309 0.82206573 -0.57923536 0.12141518 -1.44905523 0.99722837</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.05374745 -0.81078777 1.52271628 -1.21750282</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.55349668 -0.55349668 0.24542211 -0.81752498 0.84461119 1.24407059</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.04569241 1.64352998 -1.54531126 -0.55349668</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</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>
<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>
@ -214,38 +213,38 @@
<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>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A &lt;=1 0.5 4 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 1 &gt;=8 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 1 4 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 0.25 4 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &gt;=2 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 8 &gt;=2 4 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 &lt;=0.125 2 &gt;=8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 &gt;=2 &gt;=8 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 2 1 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 1 &gt;=8 0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 4 0.5 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 1 1 2 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &gt;=16 0.5 2 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 4 0.25 &gt;=4 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 2 &lt;=0.125 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 2 &lt;=0.125 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &gt;=16 &lt;=0.125 &gt;=4 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 1 &gt;=4 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 1 0.5 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=16 0.5 &gt;=4 4</span>
<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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "id" and "tobr"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.2862535 0.4403920 0.1444208 0.3173991 -0.2309563 0.1336952</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.2873676 0.4906058 -0.7522185 0.0302830</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.02072625 -0.53283992 0.56658881 -0.27325161 -0.60171721 -0.60171721</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.51272334 0.99239255 -0.70457864 0.66312613</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 2 1 1 1 -0.7522185</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 8 &lt;=0.125 2 &gt;=8 -0.2873676</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A &lt;=1 0.5 4 &gt;=8 -0.2862535</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 4 &gt;=2 1 2 -0.2309563</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 1 &gt;=8 0.25 0.0302830</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 8 &gt;=2 4 0.5 0.1336952</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 1 4 0.5 0.1444208</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 0.25 4 &gt;=8 0.3173991</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 1 &gt;=8 2 0.4403920</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 &gt;=2 &gt;=8 1 0.4906058</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 1 0.5 1 4 -0.70457864</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 2 &lt;=0.125 2 4 -0.60171721</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 2 &lt;=0.125 2 4 -0.60171721</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 1 1 2 &lt;=0.5 -0.53283992</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 4 0.25 &gt;=4 &lt;=0.5 -0.27325161</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 4 0.5 2 4 -0.02072625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &gt;=16 &lt;=0.125 &gt;=4 &gt;=16 0.51272334</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &gt;=16 0.5 2 &gt;=16 0.56658881</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=16 0.5 &gt;=4 4 0.66312613</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 8 1 &gt;=4 &gt;=16 0.99239255</span>
<span class="r-in"><span></span></span>
<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>
<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">%&gt;%</a></span></span></span>
@ -257,17 +256,17 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C 16 1 4 0.5 0.1444208 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 F 8 &gt;=2 4 0.5 0.1336952 0.01072556</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 J 8 1 &gt;=8 0.25 0.0302830 0.11413776</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 0.25 4 &gt;=8 0.3173991 0.17297837</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 B 8 1 &gt;=8 2 0.4403920 0.29597121</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 H 8 &gt;=2 &gt;=8 1 0.4906058 0.34618501</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 E 4 &gt;=2 1 2 -0.2309563 0.37537710</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 A &lt;=1 0.5 4 &gt;=8 -0.2862535 0.43067425</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 G 8 &lt;=0.125 2 &gt;=8 -0.2873676 0.43178836</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 I 2 1 1 1 -0.7522185 0.89663924</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C &gt;=16 0.5 2 &gt;=16 0.56658881 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 G &gt;=16 &lt;=0.125 &gt;=4 &gt;=16 0.51272334 0.05386547</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 J &gt;=16 0.5 &gt;=4 4 0.66312613 0.09653732</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 H 8 1 &gt;=4 &gt;=16 0.99239255 0.42580374</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 A 4 0.5 2 4 -0.02072625 0.58731506</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 D 4 0.25 &gt;=4 &lt;=0.5 -0.27325161 0.83984042</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 B 1 1 2 &lt;=0.5 -0.53283992 1.09942873</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 E 2 &lt;=0.125 2 4 -0.60171721 1.16830602</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 F 2 &lt;=0.125 2 4 -0.60171721 1.16830602</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 I 1 0.5 1 4 -0.70457864 1.27116745</span>
<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>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<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">%&gt;%</a></span></span></span>