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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9039@9444ed6
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="">1.8.2.9038</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9039</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] 0.002 0.005 0.025 0.25 16 0.0625 0.125 0.125 0.5 >=128 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 128 0.5 0.001 0.002 32 0.01 0.0625 0.0625 0.01 </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] -1.34831284 -1.07713169 -0.60080993 0.08065244 1.31149613 -0.32962879</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.12448818 -0.12448818 0.28579306 1.92691798</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.03977575 1.83205678 0.39823196 -1.20868855 -1.02946045 1.47360058</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.61330568 -0.13945235 -0.13945235 -0.61330568</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 1 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B <=8 0.125 4 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 16 0.25 >=8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D <=8 0.25 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E <=8 0.125 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F <=8 0.5 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=8 2 1 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 2 1 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I <=8 0.25 2 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 16 1 2 4</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 <=2 1 <=0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 32 0.025 <=0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=2 0.5 2 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 64 >=2 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 0.25 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 4 0.25 <=0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 32 0.125 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.25 <=0.5 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 64 >=2 8 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 64 1 4 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] 0.3264577 -0.5360484 1.0429441 -0.3185842 -0.2191155 0.1089935</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4068767 0.1106725 -0.6355170 0.5270740</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.1805861 -0.3593922 -0.5470696 0.4524955 0.1519544 -0.3106839</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.1028200 -0.6317241 0.6651338 0.6570522</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> 9 I <=8 0.25 2 <=2 -0.6355170</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B <=8 0.125 4 <=2 -0.5360484</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=8 2 1 <=2 -0.4068767</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D <=8 0.25 2 4 -0.3185842</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E <=8 0.125 4 4 -0.2191155</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F <=8 0.5 4 4 0.1089935</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 2 1 <=2 0.1106725</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A <=8 1 2 8 0.3264577</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 16 1 2 4 0.5270740</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 16 0.25 >=8 8 1.0429441</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> 8 H 16 0.25 <=0.5 <=1 -0.6317241</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=2 0.5 2 <=1 -0.5470696</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 32 0.025 <=0.5 4 -0.3593922</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 4 0.25 <=0.5 4 -0.3106839</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A <=2 1 <=0.5 4 -0.1805861</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 32 0.125 1 4 0.1028200</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 0.25 4 2 0.1519544</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 64 >=2 1 2 0.4524955</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 64 1 4 2 0.6570522</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 64 >=2 8 <=1 0.6651338</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 16 0.25 >=8 8 1.0429441 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 J 16 1 2 4 0.5270740 0.5158701</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 A <=8 1 2 8 0.3264577 0.7164865</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 H 16 2 1 <=2 0.1106725 0.9322716</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 F <=8 0.5 4 4 0.1089935 0.9339507</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E <=8 0.125 4 4 -0.2191155 1.2620596</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 D <=8 0.25 2 4 -0.3185842 1.3615283</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 G <=8 2 1 <=2 -0.4068767 1.4498208</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B <=8 0.125 4 <=2 -0.5360484 1.5789925</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 I <=8 0.25 2 <=2 -0.6355170 1.6784611</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 0.5 2 <=1 -0.5470696 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H 16 0.25 <=0.5 <=1 -0.6317241 0.0846545</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 B 32 0.025 <=0.5 4 -0.3593922 0.1876774</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F 4 0.25 <=0.5 4 -0.3106839 0.2363857</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 A <=2 1 <=0.5 4 -0.1805861 0.3664836</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G 32 0.125 1 4 0.1028200 0.6498896</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E 16 0.25 4 2 0.1519544 0.6990240</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D 64 >=2 1 2 0.4524955 0.9995652</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J 64 1 4 2 0.6570522 1.2041218</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 I 64 >=2 8 <=1 0.6651338 1.2122034</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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