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Built site for AMR: 1.8.2.9061@eed1c14
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="">1.8.2.9060</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9061</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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@ -200,11 +200,11 @@
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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] 0.0625 0.0625 0.5 >=32 0.025 8 0.125 >=32 0.125 </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] 16 0.25 8 0.025 128 4 0.0625 0.0625 <=0.002</span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 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] -0.5687734 -0.5687734 0.1128218 1.4760124 -0.8691134 1.0216155</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.3415750 1.4760124 -0.3415750 -1.3966518</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.0547374 -0.1257265 0.8579935 -0.7792959 1.6449694 0.6612495</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.5192145 -0.5192145 -1.4962027 -0.7792959</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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@ -214,38 +214,38 @@
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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 2 4 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 32 1 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 32 0.0625 4 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 32 2 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 64 0.0625 4 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F <=4 0.125 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 8 0.125 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 32 0.25 4 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.0625 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 32 0.25 4 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 16 0.5 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B >=32 0.5 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 4 0.25 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 0.5 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 8 >=1 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 2 0.125 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 1 0.5 >=8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 2 >=1 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 >=1 >=8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 16 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] 0.07915544 0.57522152 0.34727511 0.20664625 0.56026080 -0.71078914</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.07687359 0.59727511 -0.63133944 0.05316793</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.036743946 0.196829201 -0.376851467 0.425339766 0.497315583</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] -0.848366515 -0.464960905 0.006554142 0.542471648 -0.015075399</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> 7 G 8 0.125 1 2 -1.07687359</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F <=4 0.125 4 1 -0.71078914</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.0625 2 2 -0.63133944</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 32 0.25 4 1 0.05316793</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 16 2 4 <=0.5 0.07915544</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 32 2 2 2 0.20664625</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 32 0.0625 4 16 0.34727511</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 64 0.0625 4 16 0.56026080</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 32 1 4 4 0.57522152</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 32 0.25 4 16 0.59727511</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 0.125 4 1 -0.848366515</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 1 0.5 >=8 0.5 -0.464960905</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 4 0.25 2 4 -0.376851467</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 16 0.125 4 4 -0.015075399</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 2 >=1 4 2 0.006554142</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 16 0.5 4 1 0.036743946</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B >=32 0.5 1 8 0.196829201</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 0.5 4 4 0.425339766</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 8 >=1 4 4 0.497315583</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 >=1 >=8 1 0.542471648</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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@ -257,17 +257,17 @@
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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 32 0.0625 4 16 0.34727511 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 D 32 2 2 2 0.20664625 0.1406289</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E 64 0.0625 4 16 0.56026080 0.2129857</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B 32 1 4 4 0.57522152 0.2279464</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 H 32 0.25 4 16 0.59727511 0.2500000</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A 16 2 4 <=0.5 0.07915544 0.2681197</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 J 32 0.25 4 1 0.05316793 0.2941072</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 I 16 0.0625 2 2 -0.63133944 0.9786145</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 F <=4 0.125 4 1 -0.71078914 1.0580643</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 G 8 0.125 1 2 -1.07687359 1.4241487</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 0.25 2 4 -0.376851467 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G 1 0.5 >=8 0.5 -0.464960905 0.08810944</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 J 16 0.125 4 4 -0.015075399 0.36177607</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 H 2 >=1 4 2 0.006554142 0.38340561</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 A 16 0.5 4 1 0.036743946 0.41359541</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 2 0.125 4 1 -0.848366515 0.47151505</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 B >=32 0.5 1 8 0.196829201 0.57368067</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D 16 0.5 4 4 0.425339766 0.80219123</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E 8 >=1 4 4 0.497315583 0.87416705</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 I 16 >=1 >=8 1 0.542471648 0.91932312</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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@ -303,11 +303,11 @@
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<footer><div class="pkgdown-footer-left">
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<p></p><p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
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<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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</div>
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<div class="pkgdown-footer-right">
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<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a></p>
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<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
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</div>
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</footer></div>
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