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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9054@6017f81
This commit is contained in:
github-actions
@ -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] 64 1 8 0.025 0.002 0.005 0.0625 16 0.01 32 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 32 1 4 256 64 4 0.002 0.025 0.5 </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] 1.3091844 0.2558741 0.7825293 -0.6783995 -1.3180848 -1.0860180</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4463328 0.9580810 -0.9104663 1.1336327</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.3241709 0.8396588 -0.1301993 0.2577439 1.4215736 1.0336304</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.2577439 -1.8693070 -1.1625023 -0.3241709</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 8 0.025 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B <=4 0.125 0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=4 >=1 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D <=4 0.125 1 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E >=16 >=1 2 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=16 0.025 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=4 0.25 4 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H >=16 0.125 0.5 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.5 0.5 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J <=4 0.25 1 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 4 <=0.125 <=0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.25 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 32 0.25 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 2 <=0.125 <=0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 8 <=0.125 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 32 0.25 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 8 0.5 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 2 >=1 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 32 <=0.125 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 16 0.25 2 2</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] -0.55426393 -0.42949279 0.62941387 -0.05490015 0.49015830 -0.12782528</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.09926391 0.26899945 0.26246847 -0.38529402</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.51912782 -0.09831951 0.63538430 -1.20290099 -0.21181627 0.27774576</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.04628481 0.49245479 0.45927606 0.12101887</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> 1 A 8 0.025 1 1 -0.55426393</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B <=4 0.125 0.5 4 -0.42949279</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J <=4 0.25 1 1 -0.38529402</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=16 0.025 1 2 -0.12782528</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=4 0.25 4 0.5 -0.09926391</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D <=4 0.125 1 >=8 -0.05490015</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.5 0.5 >=8 0.26246847</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H >=16 0.125 0.5 >=8 0.26899945</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E >=16 >=1 2 0.5 0.49015830</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=4 >=1 4 4 0.62941387</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> 4 D 2 <=0.125 <=0.5 1 -1.20290099</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 4 <=0.125 <=0.5 4 -0.51912782</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 8 <=0.125 8 1 -0.21181627</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.25 1 4 -0.09831951</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 8 0.5 1 2 0.04628481</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 16 0.25 2 2 0.12101887</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 32 0.25 2 2 0.27774576</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 32 <=0.125 4 4 0.45927606</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 2 >=1 8 2 0.49245479</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 32 0.25 1 8 0.63538430</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 <=4 >=1 4 4 0.62941387 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 E >=16 >=1 2 0.5 0.49015830 0.1392556</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 H >=16 0.125 0.5 >=8 0.26899945 0.3604144</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 I 8 0.5 0.5 >=8 0.26246847 0.3669454</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D <=4 0.125 1 >=8 -0.05490015 0.6843140</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G <=4 0.25 4 0.5 -0.09926391 0.7286778</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 F >=16 0.025 1 2 -0.12782528 0.7572391</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 J <=4 0.25 1 1 -0.38529402 1.0147079</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B <=4 0.125 0.5 4 -0.42949279 1.0589067</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A 8 0.025 1 1 -0.55426393 1.1836778</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 32 0.25 1 8 0.63538430 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H 2 >=1 8 2 0.49245479 0.1429295</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I 32 <=0.125 4 4 0.45927606 0.1761082</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F 32 0.25 2 2 0.27774576 0.3576385</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 J 16 0.25 2 2 0.12101887 0.5143654</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G 8 0.5 1 2 0.04628481 0.5890995</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B 4 0.25 1 4 -0.09831951 0.7337038</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 E 8 <=0.125 8 1 -0.21181627 0.8472006</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 A 4 <=0.125 <=0.5 4 -0.51912782 1.1545121</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D 2 <=0.125 <=0.5 1 -1.20290099 1.8382853</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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