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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9024@3102beb
This commit is contained in:
github-actions
@ -195,10 +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] 64 128 0.01 0.001 128 0.025 16 4 64 0.25 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.025 8 0.0625 16 16 1 0.125 >=32 0.25 0.002 </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] 0.8219432 0.9802175 -1.1792542 -1.7050300 0.9802175 -0.9700270</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.5053947 0.1888461 0.8219432 -0.4442511</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.9782837 0.7941806 -0.6967299 1.0071679 1.0071679 0.1552190</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.4837427 1.2201551 -0.2707555 -1.7543786</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 4 0.125 2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 8 0.25 8 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=2 1 2 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 8 1 8 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E <=2 1 2 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F <=2 <=0.025 1 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 8 0.0625 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H <=2 2 8 >=4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.125 0.5 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=16 0.5 16 >=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 16 <=0.0625 <=0.25 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B >=32 0.125 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 4 <=0.0625 <=0.25 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D >=32 >=1 0.5 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 8 0.125 2 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 4 0.25 <=0.25 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 16 <=0.0625 <=0.25 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.25 >=4 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 4 >=1 <=0.25 >=16</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J <=2 >=1 2 8</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] -0.07272768 0.02436854 0.07054523 0.81400616 -0.47677206 -1.27310062</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.30764224 0.49475116 -0.33800496 1.06457646</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.04787176 0.30260331 -0.98864537 0.73456530 0.25539334 -0.10496162</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -0.63509198 -0.05402839 0.19150191 0.34653525</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 <=0.025 1 <=0.5 -1.27310062</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E <=2 1 2 <=0.5 -0.47677206</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 8 0.125 0.5 2 -0.33800496</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 8 0.0625 1 2 -0.30764224</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 4 0.125 2 >=4 -0.07272768</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 8 0.25 8 <=0.5 0.02436854</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C <=2 1 2 >=4 0.07054523</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H <=2 2 8 >=4 0.49475116</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 8 1 8 >=4 0.81400616</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J >=16 0.5 16 >=4 1.06457646</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 <=0.25 1 -0.98864537</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 16 <=0.0625 <=0.25 1 -0.63509198</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 4 0.25 <=0.25 >=16 -0.10496162</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 4 0.25 >=4 1 -0.05402839</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 16 <=0.0625 <=0.25 >=16 -0.04787176</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 4 >=1 <=0.25 >=16 0.19150191</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E 8 0.125 2 8 0.25539334</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B >=32 0.125 1 4 0.30260331</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J <=2 >=1 2 8 0.34653525</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D >=32 >=1 0.5 8 0.73456530</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 <=2 1 2 >=4 0.07054523 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 8 0.25 8 <=0.5 0.02436854 0.04617669</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 A 4 0.125 2 >=4 -0.07272768 0.14327291</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 G 8 0.0625 1 2 -0.30764224 0.37818747</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 I 8 0.125 0.5 2 -0.33800496 0.40855018</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 H <=2 2 8 >=4 0.49475116 0.42420593</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E <=2 1 2 <=0.5 -0.47677206 0.54731729</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 D 8 1 8 >=4 0.81400616 0.74346093</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J >=16 0.5 16 >=4 1.06457646 0.99403123</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 F <=2 <=0.025 1 <=0.5 -1.27310062 1.34364585</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 <=0.25 1 -0.98864537 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 G 16 <=0.0625 <=0.25 1 -0.63509198 0.3535534</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 F 4 0.25 <=0.25 >=16 -0.10496162 0.8836838</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 H 4 0.25 >=4 1 -0.05402839 0.9346170</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 A 16 <=0.0625 <=0.25 >=16 -0.04787176 0.9407736</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 I 4 >=1 <=0.25 >=16 0.19150191 1.1801473</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E 8 0.125 2 8 0.25539334 1.2440387</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 B >=32 0.125 1 4 0.30260331 1.2912487</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 J <=2 >=1 2 8 0.34653525 1.3351806</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 D >=32 >=1 0.5 8 0.73456530 1.7232107</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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