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Built site for AMR: 1.8.2.9023@85e2fbe
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="">1.8.2.9022</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</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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@ -194,11 +194,11 @@
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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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] >=8 0.01 0.002 0.25 1 0.5 0.001 >=8 2 4 </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] 1 >=128 >=128 0.001 4 0.125 0.25 0.01 0.001 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">x</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1.017806264 -0.962121752 -1.438824265 -0.008716725 0.401892471</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] 0.196587873 -1.644128863 1.017806264 0.607197068 0.812501666</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.23800503 1.38104904 1.38104904 -1.38932783 0.56458903 -0.25187098</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.08857897 -0.84688355 -1.38932783 0.40129703</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 <=2 0.5 <=1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B >=64 0.25 >=8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=64 0.25 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 0.25 <=1 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 32 >=1 >=8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 16 >=1 <=1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=2 0.5 <=1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H <=2 <=0.125 2 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I >=64 0.25 <=1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=64 0.25 <=1 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 <=0.025 >=4 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.5 1 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 4 0.0625 1 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D >=32 1 >=4 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.125 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 8 0.0625 >=4 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.0625 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H >=32 0.0625 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.25 <=0.25 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=32 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] -0.7016722 0.7163537 0.3902942 -0.6197198 1.1177827 0.0265375</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.1746259 -1.0218701 0.1334600 0.1334600</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.14091001 -0.32396107 -0.78118181 0.85710543 0.08049237 0.41685866</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.07191455 0.18697943 -0.07834229 -0.14512615</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> 8 H <=2 <=0.125 2 0.5 -1.0218701</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A <=2 0.5 <=1 0.5 -0.7016722</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 0.25 <=1 0.5 -0.6197198</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=2 0.5 <=1 8 -0.1746259</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 16 >=1 <=1 1 0.0265375</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I >=64 0.25 <=1 8 0.1334600</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=64 0.25 <=1 8 0.1334600</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=64 0.25 4 4 0.3902942</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B >=64 0.25 >=8 8 0.7163537</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 32 >=1 >=8 8 1.1177827</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> 3 C 4 0.0625 1 <=0.25 -0.78118181</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.5 1 <=0.25 -0.32396107</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=32 0.0625 <=0.25 2 -0.14512615</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 16 <=0.025 >=4 0.5 -0.14091001</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.25 <=0.25 4 -0.07834229</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 0.0625 2 4 -0.07191455</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.125 2 4 0.08049237</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H >=32 0.0625 1 2 0.18697943</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 8 0.0625 >=4 8 0.41685866</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D >=32 1 >=4 0.5 0.85710543</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 >=64 0.25 4 4 0.3902942 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 I >=64 0.25 <=1 8 0.1334600 0.2568343</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 J >=64 0.25 <=1 8 0.1334600 0.2568343</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B >=64 0.25 >=8 8 0.7163537 0.3260595</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 F 16 >=1 <=1 1 0.0265375 0.3637567</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G <=2 0.5 <=1 8 -0.1746259 0.5649201</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E 32 >=1 >=8 8 1.1177827 0.7274885</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D 16 0.25 <=1 0.5 -0.6197198 1.0100140</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 A <=2 0.5 <=1 0.5 -0.7016722 1.0919664</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 H <=2 <=0.125 2 0.5 -1.0218701 1.4121643</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 0.0625 1 <=0.25 -0.78118181 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.5 1 <=0.25 -0.32396107 0.4572207</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 J >=32 0.0625 <=0.25 2 -0.14512615 0.6360557</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A 16 <=0.025 >=4 0.5 -0.14091001 0.6402718</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I 8 0.25 <=0.25 4 -0.07834229 0.7028395</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G 4 0.0625 2 4 -0.07191455 0.7092673</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E 4 0.125 2 4 0.08049237 0.8616742</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H >=32 0.0625 1 2 0.18697943 0.9681612</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 F 8 0.0625 >=4 8 0.41685866 1.1980405</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D >=32 1 >=4 0.5 0.85710543 1.6382872</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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