mirror of
https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9067@6f4bb60
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="">1.8.2.9066</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9067</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 +200,10 @@
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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] <=0.001 0.0625 0.01 0.005 32 0.01 4 0.025 2 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 32 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.125 16 0.001 0.002 2 64 0.5 32 0.025 16 </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] -1.3194635 -0.2327999 -0.7143765 -0.8965258 1.4065439 -0.7143765</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8600960 -0.4735882 0.6779467 1.4065439</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.37342995 0.82860681 -1.56959121 -1.39787167 0.31344820 1.17204589</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.02999087 1.00032635 -0.77215037 0.82860681</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 +213,38 @@
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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 1 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.25 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=32 0.125 4 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D >=32 0.5 <=0.5 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.125 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 4 0.5 >=8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=1 0.5 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 1 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.0625 >=8 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 4 0.125 4 2</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 32 0.025 4 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.25 4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=64 >=1 8 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 0.5 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 32 0.5 2 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=64 >=1 16 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G >=64 0.0625 16 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 32 >=1 4 0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I >=64 0.0625 16 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=64 0.025 4 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] 0.61790612 -0.10920284 -0.05949768 -0.23827191 -0.28797707 0.45880700</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.23661482 0.29204478 -0.21259079 -0.22460280</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.6576279 -0.7207257 0.3548800 -0.4303788 -0.3775652 1.1329490</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.5359322 -0.1930342 0.6774164 -0.3218457</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> 5 E 4 0.125 1 8 -0.28797707</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D >=32 0.5 <=0.5 <=0.5 -0.23827191</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G <=1 0.5 1 8 -0.23661482</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 4 0.125 4 2 -0.22460280</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.0625 >=8 <=0.5 -0.21259079</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.25 1 8 -0.10920284</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=32 0.125 4 <=0.5 -0.05949768</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 1 2 1 0.29204478</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 4 0.5 >=8 4 0.45880700</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 16 1 4 2 0.61790612</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> 2 B 4 0.25 4 1 -0.7207257</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 32 0.025 4 0.5 -0.6576279</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 0.5 2 1 -0.4303788</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 32 0.5 2 0.5 -0.3775652</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=64 0.025 4 1 -0.3218457</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 32 >=1 4 0.25 -0.1930342</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=64 >=1 8 0.5 0.3548800</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G >=64 0.0625 16 4 0.5359322</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I >=64 0.0625 16 8 0.6774164</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F >=64 >=1 16 8 1.1329490</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 +256,17 @@
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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 0.125 4 <=0.5 -0.05949768 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 4 0.25 1 8 -0.10920284 0.04970516</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I 16 0.0625 >=8 <=0.5 -0.21259079 0.15309311</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 J 4 0.125 4 2 -0.22460280 0.16510512</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 G <=1 0.5 1 8 -0.23661482 0.17711714</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 D >=32 0.5 <=0.5 <=0.5 -0.23827191 0.17877424</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E 4 0.125 1 8 -0.28797707 0.22847939</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 1 2 1 0.29204478 0.35154246</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 F 4 0.5 >=8 4 0.45880700 0.51830468</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A 16 1 4 2 0.61790612 0.67740380</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 >=1 8 0.5 0.3548800 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G >=64 0.0625 16 4 0.5359322 0.1810522</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 I >=64 0.0625 16 8 0.6774164 0.3225364</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 H 32 >=1 4 0.25 -0.1930342 0.5479142</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 J >=64 0.025 4 1 -0.3218457 0.6767257</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 E 32 0.5 2 0.5 -0.3775652 0.7324451</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 F >=64 >=1 16 8 1.1329490 0.7780690</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D 16 0.5 2 1 -0.4303788 0.7852588</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 A 32 0.025 4 0.5 -0.6576279 1.0125079</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 B 4 0.25 4 1 -0.7207257 1.0756057</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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