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Built site for AMR: 1.8.2.9045@d2ceebe
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="">1.8.2.9044</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9045</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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@ -195,10 +195,10 @@
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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] 0.01 32 2 >=128 8 32 16 8 0.5 0.25 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.001 0.002 0.002 2 1 64 0.002 1 0.0625 >=128 </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] -2.0808837 0.7765483 -0.2050619 1.2673534 0.2857432 0.7765483</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.5311458 0.2857432 -0.6958670 -0.9412696</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.1348498 -0.9789525 -0.9789525 0.5746863 0.4187891 1.3541728</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.9789525 0.4187891 -0.2048001 1.5100701</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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@ -208,38 +208,38 @@
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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 >=4 4 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 32 0.125 1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 4 0.5 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 32 0.25 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.25 0.25 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 32 0.0625 0.25 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 32 1 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 32 0.25 0.5 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 1 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 4 0.125 0.25 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 0.5 4 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 16 <=0.025 0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 2 <=0.025 8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 4 0.125 0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 2 >=1 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 2 <=0.025 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 2 0.125 0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.125 16 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 >=1 16 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 2 0.125 1 8</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] 1.0408682 -0.2106031 0.2372580 0.6330929 -1.1062738 -0.2408099</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.2660010 -0.2183470 0.4388309 -0.8400171</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.20652090 -0.20306573 -0.09021092 -0.09638800 0.19034356 -0.69864513</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.54726673 0.52516844 1.30747940 -0.18089398</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> 5 E 4 0.25 0.25 0.25 -1.1062738</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 4 0.125 0.25 1 -0.8400171</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 32 0.0625 0.25 2 -0.2408099</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 32 0.25 0.5 0.5 -0.2183470</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 32 0.125 1 0.5 -0.2106031</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 4 0.5 4 2 0.2372580</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 32 1 0.5 1 0.2660010</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 1 1 2 0.4388309</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 32 0.25 4 2 0.6330929</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 8 >=4 4 >=4 1.0408682</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> 6 F 2 <=0.025 4 2 -0.69864513</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 2 0.125 0.5 4 -0.54726673</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 4 0.5 4 <=1 -0.20652090</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 16 <=0.025 0.5 4 -0.20306573</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 2 0.125 1 8 -0.18089398</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 4 0.125 0.5 8 -0.09638800</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 2 <=0.025 8 8 -0.09021092</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 2 >=1 4 4 0.19034356</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.125 16 8 0.52516844</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 >=1 16 8 1.30747940</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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@ -251,17 +251,17 @@
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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 0.5 4 2 0.2372580 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G 32 1 0.5 1 0.2660010 0.02874298</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I 16 1 1 2 0.4388309 0.20157281</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 32 0.25 4 2 0.6330929 0.39583483</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 B 32 0.125 1 0.5 -0.2106031 0.44786118</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H 32 0.25 0.5 0.5 -0.2183470 0.45560507</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 F 32 0.0625 0.25 2 -0.2408099 0.47806797</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 A 8 >=4 4 >=4 1.0408682 0.80361015</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J 4 0.125 0.25 1 -0.8400171 1.07727511</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 E 4 0.25 0.25 0.25 -1.1062738 1.34353185</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 2 <=0.025 8 8 -0.09021092 0.000000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 D 4 0.125 0.5 8 -0.09638800 0.006177085</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 J 2 0.125 1 8 -0.18089398 0.090683063</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B 16 <=0.025 0.5 4 -0.20306573 0.112854815</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 A 4 0.5 4 <=1 -0.20652090 0.116309983</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E 2 >=1 4 4 0.19034356 0.280554474</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 2 0.125 0.5 4 -0.54726673 0.457055812</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 F 2 <=0.025 4 2 -0.69864513 0.608434208</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 H 4 0.125 16 8 0.52516844 0.615379363</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 I 16 >=1 16 8 1.30747940 1.397690314</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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