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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9012@955f9d7
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="">1.8.2.9011</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9012</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] 32 0.25 0.005 0.002 >=256 0.125 >=256 1 32 0.025</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.025 2 0.005 32 0.01 64 <=0.001 >=128 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] >=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] 0.80748877 -0.30231828 -1.19711705 -1.40670064 1.28312036 -0.46086214</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.28312036 0.01476945 0.80748877 -0.82898960</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.7904724 0.1587950 -1.1391209 0.7594139 -0.9889662 0.9095687</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.4877694 1.0597234 0.4591045 1.0597234</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 16 0.25 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 8 0.125 4 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 2 >=2 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 4 0.25 <=0.25 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 0.025 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 2 0.0625 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.125 0.5 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 1 0.5 2 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 1 0.5 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.5 <=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 8 1 0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.25 0.5 16</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=2 0.5 0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 4 1 4 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E <=2 0.25 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 16 0.5 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.25 0.25 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 1 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.5 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 4 <=0.0625 0.25 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] 0.10394761 0.66349051 0.01965569 -0.28215761 0.23498276 -0.67838327</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.01166250 0.27821650 -0.10451638 -0.24689831</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.45989285 0.05711035 -0.37292235 0.12953221 -0.61206575 0.56287968</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.32111465 0.80202308 0.43288148 -1.13821691</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> 6 F 2 0.0625 1 1 -0.67838327</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 4 0.25 <=0.25 4 -0.28215761</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 8 0.5 <=0.25 1 -0.24689831</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 1 0.5 4 1 -0.10451638</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.125 0.5 16 0.01166250</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 2 >=2 1 1 0.01965569</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 16 0.25 1 1 0.10394761</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 0.025 4 4 0.23498276</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 1 0.5 2 16 0.27821650</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 8 0.125 4 16 0.66349051</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> 10 J 4 <=0.0625 0.25 2 -1.13821691</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E <=2 0.25 1 2 -0.61206575</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=2 0.5 0.5 4 -0.37292235</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.25 0.25 8 -0.32111465</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.25 0.5 16 0.05711035</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 4 1 4 <=1 0.12953221</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.5 1 4 0.43288148</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 8 1 0.5 8 0.45989285</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 16 0.5 4 2 0.56287968</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 1 2 4 0.80202308</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 >=2 1 1 0.01965569 0.000000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G 4 0.125 0.5 16 0.01166250 0.007993193</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 A 16 0.25 1 1 0.10394761 0.084291915</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 I 1 0.5 4 1 -0.10451638 0.124172073</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 16 0.025 4 4 0.23498276 0.215327070</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H 1 0.5 2 16 0.27821650 0.258560809</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 J 8 0.5 <=0.25 1 -0.24689831 0.266554002</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D 4 0.25 <=0.25 4 -0.28215761 0.301813300</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B 8 0.125 4 16 0.66349051 0.643834823</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 F 2 0.0625 1 1 -0.67838327 0.698038966</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 0.5 4 -0.37292235 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G 4 0.25 0.25 8 -0.32111465 0.0518077</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 E <=2 0.25 1 2 -0.61206575 0.2391434</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B 4 0.25 0.5 16 0.05711035 0.4300327</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 D 4 1 4 <=1 0.12953221 0.5024546</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 J 4 <=0.0625 0.25 2 -1.13821691 0.7652946</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 I 16 0.5 1 4 0.43288148 0.8058038</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 A 8 1 0.5 8 0.45989285 0.8328152</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 F 16 0.5 4 2 0.56287968 0.9358020</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 H 16 1 2 4 0.80202308 1.1749454</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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