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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9032@d10651e
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="">1.8.2.9031</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9032</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 +195,11 @@
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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] >=128 0.005 0.001 >=128 0.5 0.002 0.125 >=128 0.001 0.001</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5 0.005 0.025 0.25 0.5 4 2 256 0.005 </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">x</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.326173081 -0.625477475 -0.934930955 1.326173081 0.259978204</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] -0.801656595 -0.006570515 1.326173081 -0.934930955 -0.934930955</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.25069240 -0.97620422 -0.54742225 0.06602606 0.25069240 0.80469143</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.62002509 1.91268949 -0.97620422 -1.40498619</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 +209,38 @@
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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 <=2 <=0.0625 0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B <=2 <=0.0625 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=2 0.25 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D <=2 0.25 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 <=0.0625 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 4 1 1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=2 <=0.0625 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 1 0.5 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 4 <=0.0625 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.25 0.5 >=8</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 <=1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.5 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 8 1 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 2 0.125 4 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 2 4 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 1 0.025 <=1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 8 0.025 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 1 2 <=1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.125 <=1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 16 0.25 >=8 1</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] -0.63247597 0.12172575 0.13909708 0.17399130 -0.60692086 0.03530561</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.38107540 0.48453431 0.07749241 0.58832578</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.4941954 0.1411173 0.4018372 -0.4928375 0.8875875 -1.0556736</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.3568509 -0.1439580 -0.4546376 0.5792202</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 <=2 <=0.0625 0.5 2 -0.63247597</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 <=0.0625 0.5 1 -0.60692086</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=2 <=0.0625 1 2 -0.38107540</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 4 1 1 0.5 0.03530561</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 4 <=0.0625 1 4 0.07749241</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B <=2 <=0.0625 4 2 0.12172575</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=2 0.25 1 4 0.13909708</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D <=2 0.25 2 2 0.17399130</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 1 0.5 1 0.48453431</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.25 0.5 >=8 0.58832578</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 1 0.025 <=1 1 -1.0556736</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 2 0.125 4 0.5 -0.4928375</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.125 <=1 0.5 -0.4546376</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 8 0.025 2 1 -0.3568509</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 1 2 <=1 2 -0.1439580</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.5 4 1 0.1411173</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 8 1 4 1 0.4018372</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 16 2 <=1 2 0.4941954</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 16 0.25 >=8 1 0.5792202</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 2 4 >=4 0.8875875</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 +252,17 @@
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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 <=2 0.25 1 4 0.13909708 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B <=2 <=0.0625 4 2 0.12172575 0.01737133</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 D <=2 0.25 2 2 0.17399130 0.03489422</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 I 4 <=0.0625 1 4 0.07749241 0.06160466</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 F 4 1 1 0.5 0.03530561 0.10379147</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H 16 1 0.5 1 0.48453431 0.34543723</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 J 8 0.25 0.5 >=8 0.58832578 0.44922870</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 G <=2 <=0.0625 1 2 -0.38107540 0.52017247</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 E 4 <=0.0625 0.5 1 -0.60692086 0.74601794</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A <=2 <=0.0625 0.5 2 -0.63247597 0.77157305</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 8 1 4 1 0.4018372 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 A 16 2 <=1 2 0.4941954 0.09235825</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 J 16 0.25 >=8 1 0.5792202 0.17738302</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B 4 0.5 4 1 0.1411173 0.26071983</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 2 4 >=4 0.8875875 0.48575029</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H 1 2 <=1 2 -0.1439580 0.54579519</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 8 0.025 2 1 -0.3568509 0.75868806</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 I 16 0.125 <=1 0.5 -0.4546376 0.85647479</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 D 2 0.125 4 0.5 -0.4928375 0.89467471</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 F 1 0.025 <=1 1 -1.0556736 1.45751072</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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