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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9047@8d1679b
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="">1.8.2.9046</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9047</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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@ -195,10 +195,11 @@
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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] 0.0625 8 0.025 0.001 4 0.005 >=32 0.5 16 8 </span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.0625 32 128 0.01 0.125 8 256 <=0.002 0.005 </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-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] -0.54704720 0.77030301 -0.79582467 -1.66976537 0.58211012 -1.23279502</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.14668878 0.01753146 0.95849589 0.77030301</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.5813297 0.8047503 1.1127681 -0.9885071 -0.4273208 0.4967325</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.2667770 -1.3461046 -1.1425160 0.8047503</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 +209,38 @@
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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 0.125 8 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B <=4 0.125 2 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 32 0.25 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 32 0.125 >=16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E <=4 0.5 <=0.5 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 32 0.5 4 0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 8 1 8 8</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.25 2 <=0.25</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 64 0.25 1 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 32 0.125 >=16 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 <=4 1 8 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 16 0.5 4 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 8 0.5 1 1</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 16 <=0.125 2 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E <=4 0.25 2 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 8 1 1 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 16 <=0.125 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 8 >=2 2 4</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I >=32 >=2 >=16 <=0.5</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J <=4 >=2 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] -0.1243925 -0.7571711 0.1698681 0.3773926 -0.8983697 0.2361940</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.9061966 -0.4855236 0.1984131 0.3773926</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.029889016 0.523024563 -0.540292979 -0.632651576 -0.531264758</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] 0.045216758 -0.009037847 0.402397473 0.840490389 -0.067993008</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 0.5 <=0.5 <=0.25 -0.8983697</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B <=4 0.125 2 1 -0.7571711</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 16 0.25 2 <=0.25 -0.4855236</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A 8 0.125 8 2 -0.1243925</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 32 0.25 2 2 0.1698681</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I 64 0.25 1 2 0.1984131</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 32 0.5 4 0.5 0.2361940</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 32 0.125 >=16 2 0.3773926</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J 32 0.125 >=16 2 0.3773926</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 8 1 8 8 0.9061966</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> 4 D 16 <=0.125 2 <=0.5 -0.632651576</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C 8 0.5 1 1 -0.540292979</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E <=4 0.25 2 2 -0.531264758</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J <=4 >=2 4 1 -0.067993008</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 A <=4 1 8 1 -0.029889016</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G 16 <=0.125 4 2 -0.009037847</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F 8 1 1 4 0.045216758</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 8 >=2 2 4 0.402397473</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B 16 0.5 4 4 0.523024563</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I >=32 >=2 >=16 <=0.5 0.840490389</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 +252,17 @@
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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 0.25 2 2 0.1698681 0.00000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 I 64 0.25 1 2 0.1984131 0.02854493</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 F 32 0.5 4 0.5 0.2361940 0.06632587</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D 32 0.125 >=16 2 0.3773926 0.20752447</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 J 32 0.125 >=16 2 0.3773926 0.20752447</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 A 8 0.125 8 2 -0.1243925 0.29426068</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 H 16 0.25 2 <=0.25 -0.4855236 0.65539178</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 G 8 1 8 8 0.9061966 0.73632851</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B <=4 0.125 2 1 -0.7571711 0.92703927</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 E <=4 0.5 <=0.5 <=0.25 -0.8983697 1.06823788</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 8 0.5 1 1 -0.540292979 0.000000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 E <=4 0.25 2 2 -0.531264758 0.009028221</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 D 16 <=0.125 2 <=0.5 -0.632651576 0.092358597</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 J <=4 >=2 4 1 -0.067993008 0.472299971</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 A <=4 1 8 1 -0.029889016 0.510403963</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 G 16 <=0.125 4 2 -0.009037847 0.531255132</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 F 8 1 1 4 0.045216758 0.585509737</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H 8 >=2 2 4 0.402397473 0.942690452</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 B 16 0.5 4 4 0.523024563 1.063317542</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 I >=32 >=2 >=16 <=0.5 0.840490389 1.380783368</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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