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Built site for AMR@2.1.1.9279: 26447fe
This commit is contained in:
github-actions
@ -7,7 +7,7 @@
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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="">2.1.1.9277</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9279</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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@ -23,7 +23,7 @@
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<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
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<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
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<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
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<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
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<li><a class="dropdown-item" href="../reference/mdro.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
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<li><a class="dropdown-item" href="../articles/WHONET.html"><span class="fa fa-globe-americas"></span> Work with WHONET Data</a></li>
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<li><a class="dropdown-item" href="../articles/EUCAST.html"><span class="fa fa-exchange-alt"></span> Apply EUCAST Rules</a></li>
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<li><a class="dropdown-item" href="../reference/mo_property.html"><span class="fa fa-bug"></span> Get Taxonomy of a Microorganism</a></li>
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@ -110,30 +110,31 @@
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_sir</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">sir</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S R S R S S I R R R</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S R S S I R R R S S</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.9486833 0.9486833 -0.9486833 0.9486833 -0.9486833 -0.9486833</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.9486833 0.9486833 0.9486833 0.9486833</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.7745967 1.1618950 -0.7745967 -0.7745967 -0.7745967 1.1618950</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.1618950 1.1618950 -0.7745967 -0.7745967</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">mic</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">mic</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 0.01 0.001 >=64 2 0.25 0.001 32 0.025 0.125</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.01 <=0.001 >=64 2 0.25 <=0.001 32 0.025 0.125 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] <=0.001</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.28499921 -0.72680104 -1.32233848 1.53992165 0.64354848 0.10572458</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.32233848 1.36064701 -0.48981287 -0.07355006</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.52636230 -1.08012768 1.58136840 0.74786845 0.24776848 -1.08012768</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.41466841 -0.30599690 0.08106849 -1.08012768</span>
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<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
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<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</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> [1] 0.28499921 -0.72680104 -1.32233848 1.53992165 0.64354848 0.10572458</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.32233848 1.36064701 -0.48981287 -0.07355006</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.52636230 -1.08012768 1.58136840 0.74786845 0.24776848 -1.08012768</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.41466841 -0.30599690 0.08106849 -1.08012768</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">disk</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_disk</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">disk</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 36 38 46 21 46 7 16 40 16 16</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 46 7 16 44 16 16 12 41 13 47</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5400256 0.6784937 1.2323660 -0.4984851 1.2323660 -1.4677618</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.8446554 0.8169618 -0.8446554 -0.8446554</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.2329916 -1.1475367 -0.5981840 1.1109132 -0.5981840 -0.5981840</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.8423408 0.9277957 -0.7813016 1.2940308</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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@ -144,35 +145,35 @@
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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 R 19 >=8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 18 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 18 4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 29 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E R 18 <=1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 20 <=1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 23 >=8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 17 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 30 >=8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 21 >=8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A R 30 1 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 21 8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 20 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 30 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 25 16 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 31 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 31 1 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 18 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 17 0.5 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 17 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> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> and "tobr"</span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.21589554 -0.30783546 -0.09484977 0.54682437 -0.46411403 0.06897288</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.04421504 -0.78736460 0.59204530 0.27464080</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.58987341 -0.03053318 -0.04319558 -0.40303919 0.28644445 0.01028759</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.63115955 -0.11068385 -0.58280241 -0.34751080</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">y</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span></span>
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<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</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 R 18 <=1 2 -1.0490884</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 17 4 1 -0.6397907</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 30 >=8 1 -0.2221562</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 29 2 4 -0.2054825</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 20 <=1 8 -0.1971457</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A R 19 >=8 2 0.2038152</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G S 23 >=8 2 0.2038152</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 18 4 4 0.2121520</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 18 4 8 0.6381234</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 21 >=8 8 1.0557579</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D S 30 2 1 -0.9142137</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C R 20 1 4 -0.3370495</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H R 18 8 1 -0.3068815</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I S 17 0.5 >=8 -0.2003005</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F I 31 4 2 -0.1701325</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A R 30 1 >=8 0.1033656</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 31 1 >=8 0.1033656</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J S 17 4 4 0.2702827</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B I 21 8 4 0.5739488</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E S 25 16 4 0.8776150</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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@ -185,16 +186,16 @@
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> and "tobr"</span></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 S 18 4 8 -0.09484977 0.00000000</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 2 G S 23 >=8 2 -0.04421504 0.05063473</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 3 F R 20 <=1 8 0.06897288 0.16382265</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 4 B I 18 4 4 -0.30783546 0.21298569</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 5 A R 19 >=8 2 0.21589554 0.31074531</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 E R 18 <=1 2 -0.46411403 0.36926426</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 J I 21 >=8 8 0.27464080 0.36949057</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 D R 29 2 4 0.54682437 0.64167414</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 I R 30 >=8 1 0.59204530 0.68689506</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 H S 17 4 1 -0.78736460 0.69251483</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 C R 20 1 4 -0.04319558 0.00000000</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 2 B I 21 8 4 -0.03053318 0.01266241</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> 3 F I 31 4 2 0.01028759 0.05348318</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4 H R 18 8 1 -0.11068385 0.06748826</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5 J S 17 4 4 -0.34751080 0.30431522</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 6 E S 25 16 4 0.28644445 0.32964004</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 7 D S 30 2 1 -0.40303919 0.35984361</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 8 I S 17 0.5 >=8 -0.58280241 0.53960682</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 9 A R 30 1 >=8 0.58987341 0.63306899</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 10 G R 31 1 >=8 0.63115955 0.67435514</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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