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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9072@ba3b237
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="">1.8.2.9071</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9072</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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@ -200,10 +200,10 @@
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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] 4 0.002 >=128 0.0625 0.002 4 >=128 0.005 0.005 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 128 8 4 0.025 0.25 0.025 2 256 128 0.025</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] 0.6178077 -1.1095943 1.4054404 -0.3273515 -1.1095943 0.6178077</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.4054404 -0.9013555 -0.9013555 0.3027547</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.1267814234 0.3751651897 0.1872611313 -1.1885588733 -0.5643551025</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] -1.1885588733 -0.0006429272 1.3146854818 1.1267814234 -1.1885588733</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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@ -213,38 +213,38 @@
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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 >=16 1 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B <=4 <=0.0625 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=16 0.25 2 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D >=16 2 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E <=4 0.5 >=8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=16 0.5 2 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=4 0.5 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H >=16 2 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I <=4 0.5 >=8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J <=4 2 0.5 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 32 0.5 16 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 16 0.5 <=1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 4 >=1 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 2 0.25 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 1 0.25 8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 32 0.5 <=1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 8 <=0.0625 <=1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.5 16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.125 16 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.125 4 4</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] -0.1264094 -0.6023315 -0.2274499 0.6304399 0.3733443 -0.2074238</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.2632287 0.4909277 0.3733443 -0.4412127</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.0433511 -0.1293101 0.3461827 -0.2821777 -0.2881837 -0.1918269</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4613005 0.4590383 -0.3164093 -0.1793638</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> 2 B <=4 <=0.0625 2 4 -0.6023315</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J <=4 2 0.5 1 -0.4412127</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=4 0.5 2 2 -0.2632287</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=16 0.25 2 0.5 -0.2274499</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=16 0.5 2 <=0.25 -0.2074238</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A >=16 1 0.5 1 -0.1264094</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E <=4 0.5 >=8 8 0.3733443</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I <=4 0.5 >=8 8 0.3733443</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H >=16 2 1 4 0.4909277</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D >=16 2 1 8 0.6304399</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> 7 G 8 <=0.0625 <=1 8 -0.4613005</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.125 16 1 -0.3164093</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 1 0.25 8 4 -0.2881837</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 2 0.25 4 4 -0.2821777</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 32 0.5 <=1 1 -0.1918269</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.125 4 4 -0.1793638</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 16 0.5 <=1 2 -0.1293101</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 4 >=1 2 8 0.3461827</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.5 16 2 0.4590383</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 32 0.5 16 8 1.0433511</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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@ -256,17 +256,17 @@
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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 >=16 0.25 2 0.5 -0.2274499 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 F >=16 0.5 2 <=0.25 -0.2074238 0.02002611</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 G <=4 0.5 2 2 -0.2632287 0.03577879</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A >=16 1 0.5 1 -0.1264094 0.10104050</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 J <=4 2 0.5 1 -0.4412127 0.21376279</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 B <=4 <=0.0625 2 4 -0.6023315 0.37488162</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E <=4 0.5 >=8 8 0.3733443 0.60079418</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 I <=4 0.5 >=8 8 0.3733443 0.60079418</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 H >=16 2 1 4 0.4909277 0.71837760</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D >=16 2 1 8 0.6304399 0.85788985</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 4 >=1 2 8 0.3461827 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H 16 0.5 16 2 0.4590383 0.1128555</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 B 16 0.5 <=1 2 -0.1293101 0.4754929</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 J 8 0.125 4 4 -0.1793638 0.5255465</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 F 32 0.5 <=1 1 -0.1918269 0.5380096</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 D 2 0.25 4 4 -0.2821777 0.6283605</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E 1 0.25 8 4 -0.2881837 0.6343665</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 I 8 0.125 16 1 -0.3164093 0.6625920</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 A 32 0.5 16 8 1.0433511 0.6971683</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 G 8 <=0.0625 <=1 8 -0.4613005 0.8074832</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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