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Built site for AMR: 1.8.1.9049@63fe160
This commit is contained in:
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@ -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="">1.8.1.9047</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9049</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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@ -195,70 +195,73 @@
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</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">x</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] 0.5 4 >=128 <=0.002 0.25 32 0.25 0.025 4 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.005 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.0625 0.001 0.25 >=128 0.025 1 0.5 0.005 1 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">x</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.01781163 0.59141290 1.54741502 -1.50524970 -0.17338879 1.16501418</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.17338879 -0.80854285 0.59141290 -1.25249649</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.41123292 -1.57568929 -0.02085462 1.73584774 -0.66925895 0.36952368</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.17433453 -1.12247412 0.36952368 1.15028028</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>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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<span class="r-in"><span> amox <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">"amox"</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> cipr <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">"cipr"</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> gent <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">"gent"</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> 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 class="op">)</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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<span class="r-in"><span> amox <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">"amox"</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> cipr <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">"cipr"</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> gent <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">"gent"</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> 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 8 0.25 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 32 0.5 <=0.5 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 8 0.0625 <=0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 1 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 0.125 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 8 1 1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 32 0.0625 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.25 <=0.5 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 4 0.25 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 16 0.0625 2 1</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 2 2 <=0.25 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 2 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=16 2 <=0.25 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D <=1 0.25 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E >=16 <=0.125 <=0.25 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=16 <=0.125 4 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=1 2 <=0.25 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.25 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I <=1 1 0.5 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 2 0.5 >=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">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",</span>
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<span class="r-msg co"><span class="r-pr">#></span> "id" and "tobr"</span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.1021142 -0.0512292 -0.4408420 0.5640747 0.2717444 -0.0723823</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.3064119 -0.4761266 -0.0939276 -0.1098375</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.15641280 0.42857996 0.14992674 -0.42197963 -0.81679006 0.57661476</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.30349990 0.01816313 -0.02817569 0.55357349</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
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<span class="r-msg co"><span class="r-pr">#></span> "tobr"</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</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> 8 H 16 0.25 <=0.5 <=0.25 -0.4761266</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 8 0.0625 <=0.5 8 -0.4408420</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 16 0.0625 2 1 -0.1098375</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 4 0.25 4 1 -0.0939276</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 8 1 1 0.5 -0.0723823</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 32 0.5 <=0.5 <=0.25 -0.0512292</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 8 0.25 1 8 0.1021142</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 0.125 4 1 0.2717444</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 32 0.0625 1 8 0.3064119</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 1 1 4 0.5640747</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> 5 E >=16 <=0.125 <=0.25 0.25 -0.81679006</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D <=1 0.25 2 2 -0.42197963</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=1 2 <=0.25 4 -0.30349990</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 2 2 <=0.25 4 -0.15641280</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I <=1 1 0.5 >=16 -0.02817569</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.25 4 2 0.01816313</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=16 2 <=0.25 2 0.14992674</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 2 2 4 0.42857996</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 2 0.5 >=16 0.55357349</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=16 <=0.125 4 >=16 0.57661476</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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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>amr_distance <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</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-in"><span> check_id_C <span class="op">=</span> <span class="fu">distance_from_row</span><span class="op">(</span><span class="va">amr_distance</span>, <span class="va">id</span> <span class="op">==</span> <span class="st">"C"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></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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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span></span>
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<span class="r-in"><span> amr_distance <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</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-in"><span> check_id_C <span class="op">=</span> <span class="fu">distance_from_row</span><span class="op">(</span><span class="va">amr_distance</span>, <span class="va">id</span> <span class="op">==</span> <span class="st">"C"</span><span class="op">)</span></span></span>
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||||
<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">check_id_C</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-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 8 0.0625 <=0.5 8 -0.4408420 0.0000000</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 2 H 16 0.25 <=0.5 <=0.25 -0.4761266 0.0352847</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 3 J 16 0.0625 2 1 -0.1098375 0.3310044</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 4 I 4 0.25 4 1 -0.0939276 0.3469144</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 5 F 8 1 1 0.5 -0.0723823 0.3684596</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 B 32 0.5 <=0.5 <=0.25 -0.0512292 0.3896127</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 A 8 0.25 1 8 0.1021142 0.5429562</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 E 16 0.125 4 1 0.2717444 0.7125863</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 G 32 0.0625 1 8 0.3064119 0.7472539</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 D 16 1 1 4 0.5640747 1.0049167</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> id amox cipr gent tobr amr_distance check_id_C</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C >=16 2 <=0.25 2 0.14992674 0.0000000</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2 H 4 0.25 4 2 0.01816313 0.1317636</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3 I <=1 1 0.5 >=16 -0.02817569 0.1781024</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 B 4 2 2 4 0.42857996 0.2786532</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 A 2 2 <=0.25 4 -0.15641280 0.3063395</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 J 8 2 0.5 >=16 0.55357349 0.4036468</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 F >=16 <=0.125 4 >=16 0.57661476 0.4266880</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 G <=1 2 <=0.25 4 -0.30349990 0.4534266</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 D <=1 0.25 2 2 -0.42197963 0.5719064</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 E >=16 <=0.125 <=0.25 0.25 -0.81679006 0.9667168</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>
|
||||
<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">%>%</a></span></span></span>
|
||||
|
||||
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