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Built site for AMR: 1.8.2.9049@496c08d

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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="">1.8.2.9047</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9049</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">
@ -82,6 +82,11 @@
Get properties of an antibiotic
</a>
<a class="dropdown-item" href="../reference/av_property.html">
<span class="fa fa-capsules"></span>
Get properties of an antiviral agent
</a>
</div>
</li>
<li class="active nav-item">
@ -195,11 +200,11 @@
<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] 1 0.005 2 0.125 0.002 0.5 0.0625 0.5 &lt;=0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.002 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 0.01 0.01 2 0.125 &lt;=0.005 0.0625 &lt;=0.005 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &gt;=256 </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] 1.04271494 -0.78781830 1.28219266 0.32428178 -1.10439062 0.80323722</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.08480407 0.80323722 -1.34386834 -1.10439062</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.6440970 -0.8222686 -0.8222686 0.6440970 -0.1232464 -1.0141044</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.3150822 -1.0141044 0.8359328 1.9869478</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>
@ -209,38 +214,38 @@
<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 4 0.5 &lt;=1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 &gt;=1 2 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &gt;=16 0.5 2 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &gt;=16 0.25 2 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 8 0.25 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 4 0.25 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &gt;=16 0.5 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.25 2 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 0.5 4 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 0.025 4 0.5</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 8 0.25 2 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &gt;=32 0.125 &lt;=0.5 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &gt;=32 0.0625 &lt;=0.5 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 4 0.5 2 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 8 &lt;=0.025 2 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 0.125 &gt;=4 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 2 &lt;=0.5 &lt;=1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.5 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 16 0.0625 &lt;=0.5 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=32 0.0625 &lt;=0.5 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] -0.54407797 0.54766468 0.06869358 0.48271367 -0.27421097 -0.16444638</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.18654471 -0.08832657 0.36434257 -0.57889732</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.25292590 0.13456515 -0.22939265 0.18846902 0.04421622 0.50727140</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.62066776 0.14690263 -0.19489727 -0.22939265</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> 10 J 8 0.025 4 0.5 -0.57889732</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 4 0.5 &lt;=1 4 -0.54407797</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 8 0.25 2 1 -0.27421097</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 4 0.25 4 1 -0.16444638</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.25 2 &gt;=16 -0.08832657</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &gt;=16 0.5 2 0.5 0.06869358</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &gt;=16 0.5 2 1 0.18654471</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 4 0.5 4 8 0.36434257</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D &gt;=16 0.25 2 &gt;=16 0.48271367</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 8 &gt;=1 2 &gt;=16 0.54766468</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> 7 G 4 2 &lt;=0.5 &lt;=1 -0.62066776</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &gt;=32 0.0625 &lt;=0.5 4 -0.22939265</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=32 0.0625 &lt;=0.5 4 -0.22939265</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 16 0.0625 &lt;=0.5 8 -0.19489727</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 8 &lt;=0.025 2 16 0.04421622</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B &gt;=32 0.125 &lt;=0.5 8 0.13456515</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 4 0.5 &gt;=4 4 0.14690263</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 4 0.5 2 8 0.18846902</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 8 0.25 2 8 0.25292590</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 16 0.125 &gt;=4 8 0.50727140</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>
@ -252,17 +257,17 @@
<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 &gt;=16 0.5 2 0.5 0.06869358 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 G &gt;=16 0.5 2 1 0.18654471 0.1178511</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 H 4 0.25 2 &gt;=16 -0.08832657 0.1570202</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 F 4 0.25 4 1 -0.16444638 0.2331400</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I 4 0.5 4 8 0.36434257 0.2956490</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 E 8 0.25 2 1 -0.27421097 0.3429046</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 D &gt;=16 0.25 2 &gt;=16 0.48271367 0.4140201</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 B 8 &gt;=1 2 &gt;=16 0.54766468 0.4789711</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 A 4 0.5 &lt;=1 4 -0.54407797 0.6127716</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J 8 0.025 4 0.5 -0.57889732 0.6475909</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;=32 0.0625 &lt;=0.5 4 -0.22939265 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 J &gt;=32 0.0625 &lt;=0.5 4 -0.22939265 0.00000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 I 16 0.0625 &lt;=0.5 8 -0.19489727 0.03449538</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 E 8 &lt;=0.025 2 16 0.04421622 0.27360887</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 B &gt;=32 0.125 &lt;=0.5 8 0.13456515 0.36395780</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 H 4 0.5 &gt;=4 4 0.14690263 0.37629528</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 2 &lt;=0.5 &lt;=1 -0.62066776 0.39127511</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 D 4 0.5 2 8 0.18846902 0.41786167</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 A 8 0.25 2 8 0.25292590 0.48231854</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 F 16 0.125 &gt;=4 8 0.50727140 0.73666405</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>