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Built site for AMR: 2.0.0.9030@a4e2e25
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="">2.0.0.9028</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</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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@ -216,33 +216,28 @@
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
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<span class="r-in"><span><span class="va">sir</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'sir'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] S S S S S R R S S S</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sir' not found</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.4743416 -0.4743416 -0.4743416 -0.4743416 -0.4743416 1.8973666</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 1.8973666 -0.4743416 -0.4743416 -0.4743416</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sir' not found</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">mic</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-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
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<span class="r-in"><span><span class="va">mic</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 0.0625 >=256 64 4 0.005 <=0.001 0.125 1 </span>
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<span class="r-out co"><span class="r-pr">#></span> [10] 0.025 </span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'mic' not found</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -0.5822026 -0.3556128 1.7012899 1.3584728 0.6728385 -0.9802010</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.3781993 -0.1842043 0.3300214 -0.5822026</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'mic' not found</span>
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<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
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<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</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> [1] -0.5822026 -0.3556128 1.7012899 1.3584728 0.6728385 -0.9802010</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] -1.3781993 -0.1842043 0.3300214 -0.5822026</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'mic' not found</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">disk</span> <span class="op"><-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
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<span class="r-in"><span><span class="va">disk</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'disk'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 6 19 36 25 6 25 38 47 41 11</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'disk' not found</span>
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<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] -1.30715576 -0.43122664 0.71421913 -0.02695167 -1.30715576 -0.02695167</span>
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<span class="r-out co"><span class="r-pr">#></span> [7] 0.84897745 1.45538992 1.05111494 -0.97025994</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'disk' not found</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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@ -251,27 +246,15 @@
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<span class="r-in"><span> gent <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">"gent"</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> 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-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</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 R 31 >=16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 B S 25 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 C S 20 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 D R 18 4 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 E I 18 4 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 F R 30 >=16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 G R 31 8 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 H S 17 >=16 2</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 I R 20 <=2 <=1</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 J I 19 <=2 >=4</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'y' not found</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> and "tobr"</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.984641176 -0.173383326 -0.389565646 -0.001696925 -0.871323282</span>
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<span class="r-out co"><span class="r-pr">#></span> [6] 0.941404712 0.377224435 -0.095010969 -0.522640739 -0.249649437</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'y' not found</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op"><-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'y' not found</span>
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<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in order(y$amr_distance):</span> argument 1 is not a vector</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'y' not found</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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@ -281,19 +264,7 @@
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<span class="r-in"><span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">check_id_C</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-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> and "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 S 20 4 2 -0.389565646 0.0000000</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 I R 20 <=2 <=1 -0.522640739 0.1330751</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 J I 19 <=2 >=4 -0.249649437 0.1399162</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 B S 25 4 2 -0.173383326 0.2161823</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 H S 17 >=16 2 -0.095010969 0.2945547</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 D R 18 4 2 -0.001696925 0.3878687</span>
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<span class="r-out co"><span class="r-pr">#></span> 7 E I 18 4 <=1 -0.871323282 0.4817576</span>
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<span class="r-out co"><span class="r-pr">#></span> 8 G R 31 8 <=1 0.377224435 0.7667901</span>
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<span class="r-out co"><span class="r-pr">#></span> 9 F R 30 >=16 2 0.941404712 1.3309704</span>
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<span class="r-out co"><span class="r-pr">#></span> 10 A R 31 >=16 2 0.984641176 1.3742068</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'y' not found</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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@ -303,25 +274,10 @@
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>dist <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">dist</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-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_genus()</span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_species()</span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Calculating mean AMR distance based on columns "TCY", "IPM", and "MEM"</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 63 × 5</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: mo [4]</span></span>
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<span class="r-out co"><span class="r-pr">#></span> mo TCY IPM MEM dist</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> B_ENTRC_AVIM S S NA 0 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> B_ENTRC_AVIM S S NA 0 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> B_ENTRC_CSSL NA S NA <span style="color: #BB0000;">NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> B_ENTRC_FACM S S NA -<span style="color: #BB0000;">2.66</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> B_ENTRC_FACM S R R -<span style="color: #BB0000;">0.423</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> B_ENTRC_FACM S R R -<span style="color: #BB0000;">0.423</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> B_ENTRC_FACM NA R R 0.224</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> B_ENTRC_FACM NA R R 0.224</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> B_ENTRC_FACM NA R R 0.224</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> B_ENTRC_FACM NA R R 0.224</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 53 more rows</span></span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in filter(., mo_genus() == "Enterococcus" & mo_species() != ""):</span> <span style="color: #00BBBB;">ℹ</span> In argument: `mo_genus() == "Enterococcus" & mo_species() != ""`.</span>
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||||
<span class="r-err co"><span class="r-pr">#></span> <span style="font-weight: bold;">Caused by error:</span></span>
|
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<span class="r-err co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> in mo_genus(): argument x is missing and no column with info about</span>
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<span class="r-err co"><span class="r-pr">#></span> microorganisms could be found.</span>
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</code></pre></div>
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</div>
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</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
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