mirror of
https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9008@43c638d
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="">1.8.2.9007</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</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] 32 8 0.01 0.01 >=256 0.01 8 0.005 <=0.001</span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.125 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.001 0.125 1 >=128 0.005 >=128 0.001 0.0625 0.005 0.005 </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] 1.1315344 0.8152036 -0.7101208 -0.7101208 1.6060306 -0.7101208</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.8152036 -0.8682862 -1.2355349 -0.1337888</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.99724839 0.09165344 0.56061793 1.65486841 -0.63428112 1.65486841</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.99724839 -0.06466806 -0.63428112 -0.63428112</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 1 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B <=2 0.0625 8 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=64 0.5 8 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 0.125 >=16 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.5 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 16 0.5 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 16 0.125 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 32 0.5 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.5 1 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J <=2 0.5 2 4</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 0.5 <=0.5 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 1 <=0.0625 2 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 16 0.25 4 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 8 <=0.0625 <=0.5 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 <=0.0625 4 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 2 0.25 4 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 1 1 <=2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 1 4 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 4 <=0.0625 2 >=8</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 1 1 1 <=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] -0.30066368 -0.89674084 0.93947445 -0.07754651 0.09008074 0.30370274</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.33364342 0.04742155 0.37971141 -0.15179644</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.14820813 -0.44647774 0.81311070 -0.56450282 0.14549038 0.23021697</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.29155363 0.70353938 -0.05788192 -0.68014945</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> 2 B <=2 0.0625 8 <=1 -0.89674084</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 16 0.125 2 2 -0.33364342</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 8 >=1 1 <=1 -0.30066368</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J <=2 0.5 2 4 -0.15179644</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 0.125 >=16 <=1 -0.07754651</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 32 0.5 1 2 0.04742155</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 0.5 8 2 0.09008074</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 16 0.5 2 4 0.30370274</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 16 0.5 1 8 0.37971141</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C >=64 0.5 8 4 0.93947445</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 1 1 1 <=2 -0.68014945</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 8 <=0.0625 <=0.5 4 -0.56450282</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 1 <=0.0625 2 >=8 -0.44647774</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 1 1 <=2 -0.29155363</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 4 <=0.0625 2 >=8 -0.05788192</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 <=0.0625 4 >=8 0.14549038</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 8 0.5 <=0.5 >=8 0.14820813</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 2 0.25 4 >=8 0.23021697</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 1 4 >=8 0.70353938</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 16 0.25 4 >=8 0.81311070</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 >=64 0.5 8 4 0.93947445 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 I 16 0.5 1 8 0.37971141 0.5597630</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 F 16 0.5 2 4 0.30370274 0.6357717</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 E 4 0.5 8 2 0.09008074 0.8493937</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 H 32 0.5 1 2 0.04742155 0.8920529</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 D 16 0.125 >=16 <=1 -0.07754651 1.0170210</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 J <=2 0.5 2 4 -0.15179644 1.0912709</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 A 8 >=1 1 <=1 -0.30066368 1.2401381</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 G 16 0.125 2 2 -0.33364342 1.2731179</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 B <=2 0.0625 8 <=1 -0.89674084 1.8362153</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 16 0.25 4 >=8 0.81311070 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 H 4 1 4 >=8 0.70353938 0.1095713</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 F 2 0.25 4 >=8 0.23021697 0.5828937</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 A 8 0.5 <=0.5 >=8 0.14820813 0.6649026</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 4 <=0.0625 4 >=8 0.14549038 0.6676203</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I 4 <=0.0625 2 >=8 -0.05788192 0.8709926</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 4 1 1 <=2 -0.29155363 1.1046643</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 B 1 <=0.0625 2 >=8 -0.44647774 1.2595884</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 D 8 <=0.0625 <=0.5 4 -0.56450282 1.3776135</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 1 1 1 <=2 -0.68014945 1.4932602</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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