mirror of
https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9013@57d66cd
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="">1.8.2.9012</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9013</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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@ -195,11 +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] 0.025 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-out co"><span class="r-pr">#></span> [1] 16 0.5 32 >=128 64 16 4 1 0.25 0.025</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] -0.7904724 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-out co"><span class="r-pr">#></span> [1] 0.514153850 -0.750868464 0.767158312 1.273167238 1.020162775</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] 0.514153850 0.008144924 -0.497864001 -1.003872926 -1.844335559</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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@ -209,38 +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 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-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 64 1 8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B <=1 0.25 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=1 2 8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 8 0.25 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 2 >=4 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 64 1 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 64 0.0625 <=1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 64 0.25 8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 1 2 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 4 0.25 4 4</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] 0.45989285 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-out co"><span class="r-pr">#></span> [1] 0.78252639 -0.31251848 0.52307535 -0.17070133 -0.26327320 -0.05158778</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.45702796 0.50350189 -0.43776038 -0.11623450</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> 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-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> 7 G 64 0.0625 <=1 4 -0.45702796</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 1 2 <=0.5 -0.43776038</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B <=1 0.25 4 4 -0.31251848</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 2 >=4 2 1 -0.26327320</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 8 0.25 8 1 -0.17070133</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 4 0.25 4 4 -0.11623450</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 64 1 2 1 -0.05158778</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 64 0.25 8 4 0.50350189</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=1 2 8 8 0.52307535</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 64 1 8 4 0.78252639</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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@ -252,17 +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 <=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-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 <=1 2 8 8 0.52307535 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H 64 0.25 8 4 0.50350189 0.01957347</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 A 64 1 8 4 0.78252639 0.25945103</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 F 64 1 2 1 -0.05158778 0.57466313</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 J 4 0.25 4 4 -0.11623450 0.63930986</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 D 8 0.25 8 1 -0.17070133 0.69377669</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E 2 >=4 2 1 -0.26327320 0.78634856</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 B <=1 0.25 4 4 -0.31251848 0.83559383</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 1 2 <=0.5 -0.43776038 0.96083573</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 G 64 0.0625 <=1 4 -0.45702796 0.98010332</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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