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Built site for AMR: 1.8.2.9068@4c42a43

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2022-12-20 21:48:55 +00:00
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reference/mean_amr_distance.html
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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="">1.8.2.9067</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9068</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">
@ -200,10 +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] 0.125 16 0.001 0.002 2 64 0.5 32 0.025 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 128 0.025 0.002 2 8 0.025 2 128 0.5 </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] -0.37342995 0.82860681 -1.56959121 -1.39787167 0.31344820 1.17204589</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.02999087 1.00032635 -0.77215037 0.82860681</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.03073988 1.36755493 -0.98560777 -1.68148803 0.22171346 0.60366062</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.98560777 0.22171346 1.36755493 -0.16023370</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>
@ -213,38 +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 32 0.025 4 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 4 0.25 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &gt;=64 &gt;=1 8 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 0.5 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 32 0.5 2 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &gt;=64 &gt;=1 16 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &gt;=64 0.0625 16 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 32 &gt;=1 4 0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=64 0.0625 16 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=64 0.025 4 1</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 &gt;=4 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 &gt;=4 2 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 0.5 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 &gt;=4 4 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 0.125 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 32 0.25 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G 4 &lt;=0.0625 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 64 0.5 4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 32 2 4 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &lt;=2 0.5 4 2</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] -0.6576279 -0.7207257 0.3548800 -0.4303788 -0.3775652 1.1329490</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.5359322 -0.1930342 0.6774164 -0.3218457</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.08036866 0.51076165 -0.04318986 0.15636345 -0.75415022 0.48217462</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.97945442 0.75675773 0.20085706 -0.24975135</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> 2 B 4 0.25 4 1 -0.7207257</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 32 0.025 4 0.5 -0.6576279</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 0.5 2 1 -0.4303788</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 32 0.5 2 0.5 -0.3775652</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &gt;=64 0.025 4 1 -0.3218457</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 32 &gt;=1 4 0.25 -0.1930342</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C &gt;=64 &gt;=1 8 0.5 0.3548800</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G &gt;=64 0.0625 16 4 0.5359322</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I &gt;=64 0.0625 16 8 0.6774164</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F &gt;=64 &gt;=1 16 8 1.1329490</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 &lt;=0.0625 1 2 -0.97945442</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E 16 0.125 1 1 -0.75415022</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J &lt;=2 0.5 4 2 -0.24975135</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A 4 &gt;=4 1 4 -0.08036866</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C 16 0.5 2 2 -0.04318986</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D 16 &gt;=4 4 &lt;=0.5 0.15636345</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I 32 2 4 &lt;=0.5 0.20085706</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 32 0.25 4 4 0.48217462</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B 16 &gt;=4 2 4 0.51076165</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H 64 0.5 4 4 0.75675773</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>
@ -256,17 +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 &gt;=64 &gt;=1 8 0.5 0.3548800 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 G &gt;=64 0.0625 16 4 0.5359322 0.1810522</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 I &gt;=64 0.0625 16 8 0.6774164 0.3225364</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 H 32 &gt;=1 4 0.25 -0.1930342 0.5479142</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 J &gt;=64 0.025 4 1 -0.3218457 0.6767257</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 E 32 0.5 2 0.5 -0.3775652 0.7324451</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 F &gt;=64 &gt;=1 16 8 1.1329490 0.7780690</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 D 16 0.5 2 1 -0.4303788 0.7852588</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 A 32 0.025 4 0.5 -0.6576279 1.0125079</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 B 4 0.25 4 1 -0.7207257 1.0756057</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 0.5 2 2 -0.04318986 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 A 4 &gt;=4 1 4 -0.08036866 0.0371788</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 D 16 &gt;=4 4 &lt;=0.5 0.15636345 0.1995533</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 J &lt;=2 0.5 4 2 -0.24975135 0.2065615</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 I 32 2 4 &lt;=0.5 0.20085706 0.2440469</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F 32 0.25 4 4 0.48217462 0.5253645</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 B 16 &gt;=4 2 4 0.51076165 0.5539515</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 E 16 0.125 1 1 -0.75415022 0.7109604</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 H 64 0.5 4 4 0.75675773 0.7999476</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 G 4 &lt;=0.0625 1 2 -0.97945442 0.9362646</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>