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<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
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articles/AMR.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
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@@ -91,7 +91,7 @@
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 22 June 2025.</p>
generated on 17 July 2025.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2025-06-22</td>
<td align="center">2025-07-17</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2025-06-22</td>
<td align="center">2025-07-17</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2025-06-22</td>
<td align="center">2025-07-17</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
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articles/AMR_for_Python.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
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@@ -357,16 +357,16 @@ called since they are stored in the recipe.</p>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 394 × 24</span></span></span>
<span><span class="co">#&gt; .pred_class `.pred_Gram-negative` `.pred_Gram-positive` mo GEN TOB</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;fct&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;fct&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> Gram-positive 1.07<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> 8.93<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> Gram-p… 5 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> Gram-positive 3.17<span style="color: #949494;">e</span><span style="color: #BB0000;">- 8</span> 1.00<span style="color: #949494;">e</span>+ 0 Gram-p… 5 1</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> Gram-negative 9.99<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> 1.42<span style="color: #949494;">e</span><span style="color: #BB0000;">- 3</span> Gram-n… 5 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> Gram-positive 2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span> 1 <span style="color: #949494;">e</span>+ 0 Gram-p… 5 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> Gram-negative 9.46<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> 5.42<span style="color: #949494;">e</span><span style="color: #BB0000;">- 2</span> Gram-n… 5 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> Gram-positive 1.07<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> 8.93<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> Gram-p… 5 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> Gram-positive 2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span> 1 <span style="color: #949494;">e</span>+ 0 Gram-p… 1 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Gram-positive 2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span> 1 <span style="color: #949494;">e</span>+ 0 Gram-p… 4 4</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Gram-negative 1 <span style="color: #949494;">e</span>+ 0 2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span> Gram-n… 1 1</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> Gram-positive 6.05<span style="color: #949494;">e</span><span style="color: #BB0000;">-11</span> 1.00<span style="color: #949494;">e</span>+ 0 Gram-p… 4 4</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> Gram-positive 1.07<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> 8.93 <span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> Gram-p… 5 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> Gram-positive 3.17<span style="color: #949494;">e</span><span style="color: #BB0000;">- 8</span> 1.000<span style="color: #949494;">e</span>+ 0 Gram-p… 5 1</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> Gram-negative 9.99<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> 1.42 <span style="color: #949494;">e</span><span style="color: #BB0000;">- 3</span> Gram-n… 5 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> Gram-positive 2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span> 1 <span style="color: #949494;">e</span>+ 0 Gram-p… 5 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> Gram-negative 9.46<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> 5.42 <span style="color: #949494;">e</span><span style="color: #BB0000;">- 2</span> Gram-n… 5 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> Gram-positive 1.07<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> 8.93 <span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> Gram-p… 5 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> Gram-positive 2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span> 1 <span style="color: #949494;">e</span>+ 0 Gram-p… 1 5</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Gram-positive 2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span> 1 <span style="color: #949494;">e</span>+ 0 Gram-p… 4 4</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Gram-negative 1 <span style="color: #949494;">e</span>+ 0 2.22 <span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span> Gram-n… 1 1</span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> Gram-positive 6.05<span style="color: #949494;">e</span><span style="color: #BB0000;">-11</span> 1.000<span style="color: #949494;">e</span>+ 0 Gram-p… 4 4</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 384 more rows</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># ℹ 18 more variables: AMK &lt;int&gt;, KAN &lt;int&gt;, PEN &lt;int&gt;, OXA &lt;int&gt;, FLC &lt;int&gt;,</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># AMX &lt;int&gt;, AMC &lt;int&gt;, AMP &lt;int&gt;, TZP &lt;int&gt;, CZO &lt;int&gt;, FEP &lt;int&gt;,</span></span></span>
articles/EUCAST.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
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articles/PCA.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
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articles/WHONET.html
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -311,6 +311,12 @@ using the included <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">Country</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">Country</span>, <span class="va">AMP_ND2</span>, <span class="va">AMC_ED20</span>, <span class="va">CAZ_ED10</span>, <span class="va">CIP_ED5</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/ggplot_sir.html">ggplot_sir</a></span><span class="op">(</span>translate_ab <span class="op">=</span> <span class="st">"ab"</span>, facet <span class="op">=</span> <span class="st">"Country"</span>, datalabels <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
<pre><code><span><span class="co">#&gt; Warning: in <span style="background-color: #EEEEEE;">as.sir()</span>: 394 results in index 'Country' truncated (79%) that were</span></span>
<span><span class="co">#&gt; invalid antimicrobial interpretations: "Belgium", "France", "Germany", and</span></span>
<span><span class="co">#&gt; "The Netherlands"</span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">Note that </span><span style="color: #0000BB; background-color: #EEEEEE;">sir_calc_df()</span><span style="color: #0000BB;"> will also count dose-dependent susceptibility,</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; 'SDD', as 'SI' when </span><span style="color: #0000BB; background-color: #EEEEEE;">combine_SI = TRUE</span><span style="color: #0000BB;">. This note will be shown once for</span></span></span>
<span><span class="co"><span style="color: #0000BB;">#&gt; this session.</span></span></span></code></pre>
<p><img src="WHONET_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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articles/WISCA.html
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
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articles/datasets.html
+2 -2
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@@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
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@@ -80,7 +80,7 @@
<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
<h4 data-toc-skip class="date">22 June 2025</h4>
<h4 data-toc-skip class="date">17 July 2025</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>
articles/index.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
authors.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
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index.html
+21 -21
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@@ -33,7 +33,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -99,10 +99,10 @@
</blockquote>
<div style="display: flex; font-size: 0.8em;">
<p style="text-align:left; width: 50%;">
<small><a href="https://amr-for-r.org/">https://amr-for-r.org</a></small>
<small><a href="https://amr-for-r.org/">amr-for-r.org</a></small>
</p>
<p style="text-align:right; width: 50%;">
<small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank" class="external-link">https://doi.org/10.18637/jss.v104.i03</a></small>
<small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank" class="external-link">doi.org/10.18637/jss.v104.i03</a></small>
</p>
</div>
<p><a href="./reference/clinical_breakpoints.html#response-from-clsi-and-eucast"><img src="./endorsement_clsi_eucast.jpg" class="endorse_img" align="right" height="120"></a></p>
@@ -407,9 +407,9 @@
<span><span class="co">#&gt; # A tibble: 3 × 5</span></span>
<span><span class="co">#&gt; ward GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int</span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; </span></span>
<span><span class="co">#&gt; 1 Clinical 0.2289362 0.205-0.254 0.3147503 0.284-0.347 </span></span>
<span><span class="co">#&gt; 2 ICU 0.2902655 0.253-0.33 0.4004739 0.353-0.449 </span></span>
<span><span class="co">#&gt; 3 Outpatient 0.2 0.131-0.285 0.3676471 0.254-0.493</span></span></code></pre></div>
<span><span class="co">#&gt; 1 Clinical 0.229 0.205-0.254 0.315 0.284-0.347 </span></span>
<span><span class="co">#&gt; 2 ICU 0.290 0.253-0.33 0.400 0.353-0.449 </span></span>
<span><span class="co">#&gt; 3 Outpatient 0.2 0.131-0.285 0.368 0.254-0.493</span></span></code></pre></div>
<p>Or use <a href="https://amr-for-r.org/reference/antimicrobial_selectors.html">antimicrobial selectors</a> to select a series of antibiotic columns:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
@@ -432,29 +432,29 @@
<span><span class="co">#&gt; "Outpatient" (minimum = 30).</span></span>
<span><span class="va">out</span></span>
<span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
<span><span class="co">#&gt; ward GEN TOB AMK KAN COL</span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;</span></span>
<span><span class="co">#&gt; 1 Clinical 0.2289362 0.3147503 0.6258993 1 0.7802956</span></span>
<span><span class="co">#&gt; 2 ICU 0.2902655 0.4004739 0.6624473 1 0.8574144</span></span>
<span><span class="co">#&gt; 3 Outpatient 0.2 0.3676471 0.6052632 NA 0.8888889</span></span></code></pre></div>
<span><span class="co">#&gt; ward GEN TOB AMK KAN COL</span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;</span></span>
<span><span class="co">#&gt; 1 Clinical 0.229 0.315 0.626 1 0.780</span></span>
<span><span class="co">#&gt; 2 ICU 0.290 0.400 0.662 1 0.857</span></span>
<span><span class="co">#&gt; 3 Outpatient 0.2 0.368 0.605 NA 0.889</span></span></code></pre></div>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># transform the antibiotic columns to names:</span></span>
<span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
<span><span class="co">#&gt; ward gentamicin tobramycin amikacin kanamycin colistin</span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;</span></span>
<span><span class="co">#&gt; 1 Clinical 0.2289362 0.3147503 0.6258993 1 0.7802956</span></span>
<span><span class="co">#&gt; 2 ICU 0.2902655 0.4004739 0.6624473 1 0.8574144</span></span>
<span><span class="co">#&gt; 3 Outpatient 0.2 0.3676471 0.6052632 NA 0.8888889</span></span></code></pre></div>
<span><span class="co">#&gt; ward gentamicin tobramycin amikacin kanamycin colistin</span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;</span></span>
<span><span class="co">#&gt; 1 Clinical 0.229 0.315 0.626 1 0.780</span></span>
<span><span class="co">#&gt; 2 ICU 0.290 0.400 0.662 1 0.857</span></span>
<span><span class="co">#&gt; 3 Outpatient 0.2 0.368 0.605 NA 0.889</span></span></code></pre></div>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># transform the antibiotic column to ATC codes:</span></span>
<span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span>property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span>
<span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
<span><span class="co">#&gt; ward J01GB03 J01GB01 J01GB06 J01GB04 J01XB01</span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;</span></span>
<span><span class="co">#&gt; 1 Clinical 0.2289362 0.3147503 0.6258993 1 0.7802956</span></span>
<span><span class="co">#&gt; 2 ICU 0.2902655 0.4004739 0.6624473 1 0.8574144</span></span>
<span><span class="co">#&gt; 3 Outpatient 0.2 0.3676471 0.6052632 NA 0.8888889</span></span></code></pre></div>
<span><span class="co">#&gt; ward J01GB03 J01GB01 J01GB06 J01GB04 J01XB01</span></span>
<span><span class="co">#&gt; &lt;chr&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;</span></span>
<span><span class="co">#&gt; 1 Clinical 0.229 0.315 0.626 1 0.780</span></span>
<span><span class="co">#&gt; 2 ICU 0.290 0.400 0.662 1 0.857</span></span>
<span><span class="co">#&gt; 3 Outpatient 0.2 0.368 0.605 NA 0.889</span></span></code></pre></div>
</div>
</div>
<div class="section level2">
news/index.html
+10 -8
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -49,24 +49,26 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.0.9004" id="amr-3009004">AMR 3.0.0.9004<a class="anchor" aria-label="anchor" href="#amr-3009004"></a></h2>
<h2 class="pkg-version" data-toc-text="3.0.0.9008" id="amr-3009008">AMR 3.0.0.9008<a class="anchor" aria-label="anchor" href="#amr-3009008"></a></h2>
<p>This is primarily a bugfix release, though we added one nice feature too.</p>
<div class="section level4">
<h4 id="new-3-0-0-9004">New<a class="anchor" aria-label="anchor" href="#new-3-0-0-9004"></a></h4>
<h4 id="new-3-0-0-9008">New<a class="anchor" aria-label="anchor" href="#new-3-0-0-9008"></a></h4>
<ul><li>Integration with the <strong>tidymodels</strong> framework to allow seamless use of MIC and SIR data in modelling pipelines via <code>recipes</code>
<ul><li>
<code><a href="../reference/amr-tidymodels.html">step_mic_log2()</a></code> to transform <code>&lt;mic&gt;</code> columns with log2, and <code><a href="../reference/amr-tidymodels.html">step_sir_numeric()</a></code> to convert <code>&lt;sir&gt;</code> columns to numeric</li>
<li>
<code>tidyselect</code> helpers: <code><a href="../reference/amr-tidymodels.html">all_mic()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_mic_predictors()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_sir()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_sir_predictors()</a></code>
</li>
<li>Enables seamless use of MIC and SIR data in modelling pipelines via <code>recipes</code>
<li>New <code>tidyselect</code> helpers: <code><a href="../reference/amr-tidymodels.html">all_mic()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_mic_predictors()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_sir()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_sir_predictors()</a></code>
</li>
</ul></li>
</ul></div>
<div class="section level4">
<h4 id="changed-3-0-0-9004">Changed<a class="anchor" aria-label="anchor" href="#changed-3-0-0-9004"></a></h4>
<h4 id="changed-3-0-0-9008">Changed<a class="anchor" aria-label="anchor" href="#changed-3-0-0-9008"></a></h4>
<ul><li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> for when no antimicrobials are set</li>
<li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> to allow column names containing the <code>+</code> character (<a href="https://github.com/msberends/AMR/issues/222" class="external-link">#222</a>)</li>
<li>Fixed a bug in <code><a href="../reference/as.ab.html">as.ab()</a></code> for antimicrobial codes with a number in it if they are preceded by a space</li>
<li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> for using specific custom rules</li>
<li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> to allow any tidyselect language (<a href="https://github.com/msberends/AMR/issues/220" class="external-link">#220</a>)</li>
<li>Fixed a bug in <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a></code> when using <code>combine_SI = FALSE</code> (<a href="https://github.com/msberends/AMR/issues/213" class="external-link">#213</a>)</li>
<li>Fixed all plotting to contain a separate colour for SDD (susceptible dose-dependent)</li>
<li>Fixed some specific Dutch translations for antimicrobials</li>
<li>Updated <code><a href="../reference/random.html">random_mic()</a></code> and <code><a href="../reference/random.html">random_disk()</a></code> to set skewedness of the distribution and allow multiple microorganisms</li>
</ul></div>
pkgdown.yml
+1 -1
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@@ -10,7 +10,7 @@ articles:
PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
last_built: 2025-06-22T18:50Z
last_built: 2025-07-17T15:12Z
urls:
reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles
reference/AMR-deprecated.html
+1 -1
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/AMR-options.html
+1 -1
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/AMR.html
+1 -1
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@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/WHOCC.html
+1 -1
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/WHONET.html
+1 -1
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
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reference/ab_from_text.html
+1 -1
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
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reference/ab_property.html
+1 -1
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
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reference/add_custom_antimicrobials.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
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reference/add_custom_microorganisms.html
+1 -1
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
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reference/age.html
+11 -11
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
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@@ -112,16 +112,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1980-02-27 45 45.31507 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 71 71.90685 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 75 75.80274 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 38 38.88493 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 92 92.58904 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.23014 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 28 28.99726 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 61 61.76438 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.10137 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 72 72.60274 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1980-02-27 45 45.38356 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 71 71.97534 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 75 75.87123 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 38 38.95342 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 92 92.65753 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.29863 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.06575 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 61 61.83288 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.16986 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 72 72.67123 47</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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reference/age_groups.html
+8 -2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
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@@ -147,7 +147,13 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: ggplot2</span>
<span class="r-plt img"><img src="age_groups-1.png" alt="" width="700" height="433"></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">as.sir()</span>: 271 results in index 'age_group' truncated (100%) that were</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> invalid antimicrobial interpretations: "0-11", "12-24", "25-54", "55-74",</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> and "75+"</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in ggplot2::geom_col(data = function(x) { sir_df(data = x, translate_ab = translate_ab, language = language, minimum = minimum, combine_SI = combine_SI)}, mapping = utils::modifyList(ggplot2::aes(), list(x = str2lang(x), y = str2lang(y), fill = str2lang(fill))), position = position, ...):</span> Problem while computing layer data.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Error occurred in the 1st layer.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Caused by error in `sir_df()`:</span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> incorrect number of dimensions</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>
reference/amr-tidymodels.html
+3 -3
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
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@@ -125,10 +125,10 @@ may affect the computations for subsequent operations.</p></dd>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Attaching packages</span> ────────────────────────────────────── tidymodels 1.3.0 ──</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom </span> 1.0.8 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample </span> 1.3.0</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials </span> 1.4.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tibble </span> 3.3.0</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">infer </span> 1.0.8 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr </span> 1.3.1</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">infer </span> 1.0.9 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr </span> 1.3.1</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata </span> 1.4.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune </span> 1.3.0</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">parsnip </span> 1.3.2 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflows </span> 1.2.0</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">purrr </span> 1.0.4 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflowsets</span> 1.1.1</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">purrr </span> 1.1.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflowsets</span> 1.1.1</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes </span> 1.3.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick </span> 1.3.2</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Conflicts</span> ───────────────────────────────────────── tidymodels_conflicts() ──</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">purrr</span>::<span style="color: #00BB00;">discard()</span> masks <span style="color: #0000BB;">scales</span>::discard()</span>
reference/antibiogram.html
+1 -1
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@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/antimicrobial_selectors.html
+1 -1
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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/antimicrobials.html
+1 -1
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/as.ab.html
+1 -1
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/as.av.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/as.disk.html
+1 -1
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/as.mic-3.png
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reference/as.mic.html
+1 -1
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/as.mo.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/as.sir.html
+11 -6
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -128,7 +128,8 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>For using on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: names of columns to apply <code>as.sir()</code> on (supports tidy selection such as <code>column1:column4</code>). Otherwise: arguments passed on to methods.</p></dd>
<dd><p>For using on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: selection of columns to apply <code>as.sir()</code> to. Supports <a href="https://tidyselect.r-lib.org/reference/starts_with.html" class="external-link">tidyselect language</a> such as <code>where(is.mic)</code>, <code>starts_with(...)</code>, or <code>column1:column4</code>, and can thus also be <a href="antimicrobial_selectors.html">antimicrobial selectors</a> such as <code>as.sir(df, penicillins())</code>.</p>
<p>Otherwise: arguments passed on to methods.</p></dd>
<dt id="arg-threshold">threshold<a class="anchor" aria-label="anchor" href="#arg-threshold"></a></dt>
@@ -414,10 +415,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-06-22 <span style="color: #949494;">18:51:08</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-06-22 <span style="color: #949494;">18:51:08</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-06-22 <span style="color: #949494;">18:51:08</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-06-22 <span style="color: #949494;">18:51:08</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-07-17 <span style="color: #949494;">15:13:14</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-07-17 <span style="color: #949494;">15:13:15</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-07-17 <span style="color: #949494;">15:13:15</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-07-17 <span style="color: #949494;">15:13:16</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>
@@ -446,9 +447,12 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">|</span> <span class="fu"><a href="as.disk.html">is.disk</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</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="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">amoxicillin</span><span class="op">:</span><span class="va">tobra</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="va">amoxicillin</span><span class="op">:</span><span class="va">tobra</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="antimicrobial_selectors.html">aminopenicillins</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="co"># approaches that all work with additional arguments:</span></span></span>
<span class="r-in"><span> <span class="va">df_long</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="co"># given a certain data type, e.g. MIC values</span></span></span>
@@ -544,6 +548,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-in"><span> <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">cipro</span><span class="op">:</span><span class="va">genta</span><span class="op">)</span>, <span class="va">as.sir</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminopenicillins()</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">'</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
reference/atc_online.html
+1 -1
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/av_from_text.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/av_property.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/availability.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/bug_drug_combinations.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/clinical_breakpoints.html
+1 -1
View File
@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/count.html
+4 -16
View File
@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -245,21 +245,9 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 12 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward antibiotic interpretation value</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ord&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical AMX SI 357</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical AMX R 487</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical CIP SI 741</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical CIP R 128</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU AMX SI 158</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU AMX R 270</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU CIP SI 362</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU CIP R 85</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Outpatient AMX SI 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Outpatient AMX R 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> Outpatient CIP SI 78</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> Outpatient CIP R 15</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">as.sir()</span>: 2000 results in index 'ward' truncated (100%) that were</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> invalid antimicrobial interpretations: "Clinical", "ICU", and "Outpatient"</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in count_df():</span> incorrect number of dimensions</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>
reference/custom_eucast_rules.html
+1 -1
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/custom_mdro_guideline.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/dosage.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/esbl_isolates.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/eucast_rules.html
+1 -1
View File
@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/example_isolates.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/example_isolates_unclean.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/export_ncbi_biosample.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/first_isolate.html
+1 -1
View File
@@ -9,7 +9,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/g.test.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/get_episode.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/ggplot_pca.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/ggplot_sir-10.png
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reference/ggplot_sir.html
+22 -12
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -59,10 +59,10 @@
<span> fill <span class="op">=</span> <span class="st">"interpretation"</span>, facet <span class="op">=</span> <span class="cn">NULL</span>, breaks <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">0.1</span><span class="op">)</span>,</span>
<span> limits <span class="op">=</span> <span class="cn">NULL</span>, translate_ab <span class="op">=</span> <span class="st">"name"</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> minimum <span class="op">=</span> <span class="fl">30</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, nrow <span class="op">=</span> <span class="cn">NULL</span>, colours <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S</span>
<span> <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SI <span class="op">=</span> <span class="st">"#3CAEA3"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, IR <span class="op">=</span> <span class="st">"#ED553B"</span>, R <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
<span> datalabels <span class="op">=</span> <span class="cn">TRUE</span>, datalabels.size <span class="op">=</span> <span class="fl">2.5</span>, datalabels.colour <span class="op">=</span> <span class="st">"grey15"</span>,</span>
<span> title <span class="op">=</span> <span class="cn">NULL</span>, subtitle <span class="op">=</span> <span class="cn">NULL</span>, caption <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> x.title <span class="op">=</span> <span class="st">"Antimicrobial"</span>, y.title <span class="op">=</span> <span class="st">"Proportion"</span>, <span class="va">...</span><span class="op">)</span></span>
<span> <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SI <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, IR <span class="op">=</span> <span class="st">"#ED553B"</span>,</span>
<span> R <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>, datalabels <span class="op">=</span> <span class="cn">TRUE</span>, datalabels.size <span class="op">=</span> <span class="fl">2.5</span>,</span>
<span> datalabels.colour <span class="op">=</span> <span class="st">"grey15"</span>, title <span class="op">=</span> <span class="cn">NULL</span>, subtitle <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> caption <span class="op">=</span> <span class="cn">NULL</span>, x.title <span class="op">=</span> <span class="st">"Antimicrobial"</span>, y.title <span class="op">=</span> <span class="st">"Proportion"</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">geom_sir</span><span class="op">(</span>position <span class="op">=</span> <span class="cn">NULL</span>, x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"antibiotic"</span>, <span class="st">"interpretation"</span><span class="op">)</span>,</span>
<span> fill <span class="op">=</span> <span class="st">"interpretation"</span>, translate_ab <span class="op">=</span> <span class="st">"name"</span>, minimum <span class="op">=</span> <span class="fl">30</span>,</span>
@@ -256,18 +256,23 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">age_group</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu">ggplot_sir</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"age_group"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 6 rows containing missing values or values outside the scale range</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (`geom_col()`).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 6 rows containing missing values or values outside the scale range</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (`geom_text()`).</span>
<span class="r-plt img"><img src="ggplot_sir-8.png" alt="" width="700" height="433"></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">as.sir()</span>: 271 results in index 'age_group' truncated (100%) that were</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> invalid antimicrobial interpretations: "0-11", "12-24", "25-54", "55-74",</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> and "75+"</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in ggplot2::geom_col(data = function(x) { sir_df(data = x, translate_ab = translate_ab, language = language, minimum = minimum, combine_SI = combine_SI)}, mapping = utils::modifyList(ggplot2::aes(), list(x = str2lang(x), y = str2lang(y), fill = str2lang(fill))), position = position, ...):</span> Problem while computing layer data.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Error occurred in the 1st layer.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Caused by error in `sir_df()`:</span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> incorrect number of dimensions</span>
<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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&amp;&amp;</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>
<span class="r-in"><span> <span class="co"># a shorter version which also adjusts data label colours:</span></span></span>
<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">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">NIT</span>, <span class="va">FOS</span>, <span class="va">TMP</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu">ggplot_sir</span><span class="op">(</span>colours <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="ggplot_sir-9.png" alt="" width="700" height="433"></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in ggplot2::geom_col(data = function(x) { sir_df(data = x, translate_ab = translate_ab, language = language, minimum = minimum, combine_SI = combine_SI)}, mapping = utils::modifyList(ggplot2::aes(), list(x = str2lang(x), y = str2lang(y), fill = str2lang(fill))), position = position, ...):</span> Problem while converting geom to grob.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Error occurred in the 1st layer.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Caused by error:</span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Unknown colour name: FALSE</span>
<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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span> <span class="op">&amp;&amp;</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>
<span class="r-in"><span> <span class="co"># it also supports groups (don't forget to use the group var on `x` or `facet`):</span></span></span>
<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">%&gt;%</a></span></span></span>
@@ -285,7 +290,12 @@
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_is_gram_negative()</span></span>
<span class="r-plt img"><img src="ggplot_sir-10.png" alt="" width="700" height="433"></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">as.sir()</span>: 700 results in index 'ward' truncated (100%) that were</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> invalid antimicrobial interpretations: "Clinical" and "ICU"</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in ggplot2::geom_col(data = function(x) { sir_df(data = x, translate_ab = translate_ab, language = language, minimum = minimum, combine_SI = combine_SI)}, mapping = utils::modifyList(ggplot2::aes(), list(x = str2lang(x), y = str2lang(y), fill = str2lang(fill))), position = position, ...):</span> Problem while computing layer data.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Error occurred in the 1st layer.</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">Caused by error in `sir_df()`:</span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> incorrect number of dimensions</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>
reference/guess_ab_col.html
+1 -1
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/index.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/intrinsic_resistant.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/italicise_taxonomy.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/join.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/key_antimicrobials.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/kurtosis.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/like.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/mdro.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/mean_amr_distance.html
+2 -2
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -75,7 +75,7 @@
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Variables to select. Supports <a href="https://tidyselect.r-lib.org/reference/language.html" class="external-link">tidyselect language</a> (such as <code>column1:column4</code> and <code>where(is.mic)</code>), and can thus also be <a href="antimicrobial_selectors.html">antimicrobial selectors</a>.</p></dd>
<dd><p>Variables to select. Supports <a href="https://tidyselect.r-lib.org/reference/starts_with.html" class="external-link">tidyselect language</a> such as <code>where(is.mic)</code>, <code>starts_with(...)</code>, or <code>column1:column4</code>, and can thus also be <a href="antimicrobial_selectors.html">antimicrobial selectors</a>.</p></dd>
<dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt>
reference/microorganisms.codes.html
+1 -1
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/microorganisms.groups.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/microorganisms.html
+1 -1
View File
@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/mo_matching_score.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/mo_property.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/mo_source.html
+1 -1
View File
@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/pca.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/plot-2.png
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reference/plot.html
+22 -22
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@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -66,17 +66,17 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span></span>
<span><span class="fu">scale_fill_mic</span><span class="op">(</span>keep_operators <span class="op">=</span> <span class="st">"edges"</span>, mic_range <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">scale_x_sir</span><span class="op">(</span>colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>,</span>
<span> <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op">==</span> <span class="st">"EUCAST"</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">scale_x_sir</span><span class="op">(</span>colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, R</span>
<span> <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op">==</span> <span class="st">"EUCAST"</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">scale_colour_sir</span><span class="op">(</span>colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>,</span>
<span> <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op">==</span> <span class="st">"EUCAST"</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">scale_colour_sir</span><span class="op">(</span>colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span></span>
<span> <span class="st">"#F6D55C"</span>, R <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op">==</span> <span class="st">"EUCAST"</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">scale_fill_sir</span><span class="op">(</span>colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>,</span>
<span> <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op">==</span> <span class="st">"EUCAST"</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">scale_fill_sir</span><span class="op">(</span>colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>,</span>
<span> R <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op">==</span> <span class="st">"EUCAST"</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for class 'mic'</span></span>
<span><span class="fu">plot</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>,</span>
@@ -84,8 +84,8 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span> main <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>, language</span>
<span> <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
<span> xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Minimum Inhibitory Concentration (mg/L)"</span>, language <span class="op">=</span></span>
<span> <span class="va">language</span><span class="op">)</span>, colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> <span class="va">language</span><span class="op">)</span>, colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, R</span>
<span> <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
@@ -95,8 +95,8 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span> title <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span><span class="op">)</span>, ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>,</span>
<span> language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
<span> xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Minimum Inhibitory Concentration (mg/L)"</span>, language <span class="op">=</span></span>
<span> <span class="va">language</span><span class="op">)</span>, colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> <span class="va">language</span><span class="op">)</span>, colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, R</span>
<span> <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
@@ -105,8 +105,8 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span> ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>, language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
<span> xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Disk diffusion diameter (mm)"</span>, language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
<span> mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>, guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>,</span>
<span> colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, R <span class="op">=</span></span>
<span> <span class="st">"#ED553B"</span><span class="op">)</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
@@ -115,8 +115,8 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span> title <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span><span class="op">)</span>, ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>,</span>
<span> language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>, xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Disk diffusion diameter (mm)"</span>,</span>
<span> language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>, guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>,</span>
<span> colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, R <span class="op">=</span></span>
<span> <span class="st">"#ED553B"</span><span class="op">)</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
<span> breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
@@ -129,8 +129,8 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span><span class="co"># S3 method for class 'sir'</span></span>
<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">object</span>, title <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span><span class="op">)</span>,</span>
<span> xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Antimicrobial Interpretation"</span>, language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
<span> ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>, language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
<span> colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
<span> ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>, language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>, colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S</span>
<span> <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, R <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
<span> language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">facet_sir</span><span class="op">(</span>facet <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"interpretation"</span>, <span class="st">"antibiotic"</span><span class="op">)</span>, nrow <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span>
@@ -138,8 +138,8 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span><span class="fu">scale_y_percent</span><span class="op">(</span>breaks <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, <span class="fl">0.1</span><span class="op">)</span>,</span>
<span> limits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">scale_sir_colours</span><span class="op">(</span><span class="va">...</span>, <span class="va">aesthetics</span>, colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>,</span>
<span> <span class="st">"#ED553B"</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="fu">scale_sir_colours</span><span class="op">(</span><span class="va">...</span>, <span class="va">aesthetics</span>, colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span></span>
<span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, R <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">theme_sir</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
reference/proportion.html
+4 -16
View File
@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -384,21 +384,9 @@ resistance() should be used to calculate resistance, susceptibility() should be
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu">sir_df</span><span class="op">(</span>translate <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 12 × 7</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward antibiotic interpretation value ci_min ci_max isolates</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ord&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical AMX SI 0.423 0.389 0.457 357</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical AMX R 0.577 0.543 0.611 487</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical CIP SI 0.853 0.827 0.876 741</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical CIP R 0.147 0.124 0.173 128</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU AMX SI 0.369 0.323 0.417 158</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU AMX R 0.631 0.583 0.677 270</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU CIP SI 0.810 0.770 0.845 362</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU CIP R 0.190 0.155 0.230 85</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Outpatient AMX SI 0.397 0.288 0.515 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Outpatient AMX R 0.603 0.485 0.712 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> Outpatient CIP SI 0.839 0.748 0.907 78</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> Outpatient CIP R 0.161 0.093<span style="text-decoration: underline;">2</span> 0.252 15</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">as.sir()</span>: 2000 results in index 'ward' truncated (100%) that were</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> invalid antimicrobial interpretations: "Clinical", "ICU", and "Outpatient"</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in sir_df():</span> incorrect number of dimensions</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>
reference/random.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/resistance_predict.html
+1 -1
View File
@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/skewness.html
+1 -1
View File
@@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/top_n_microorganisms.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
reference/translate.html
+1 -1
View File
@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9008</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
search.json
+1 -1
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[{"path":"https://amr-for-r.org/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) reliable data thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"Conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"Conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #> patient_id hospital date bacteria AMX AMC CIP GEN #> <chr> <chr> <date> <chr> <chr> <chr> <chr> <chr> #> 1 J3 A 2012-11-21 E. coli R I S S #> 2 R7 A 2018-04-03 K. pneumoniae R I S S #> 3 P3 A 2014-09-19 E. coli R S S S #> 4 P10 A 2015-12-10 E. coli S I S S #> 5 B7 A 2015-03-02 E. coli S S S S #> 6 W3 A 2018-03-31 S. aureus R S R S #> 7 J8 A 2016-06-14 E. coli R S S S #> 8 M3 A 2015-10-25 E. coli R S S S #> 9 J3 A 2019-06-19 E. coli S S S S #> 10 G6 A 2015-04-27 S. aureus S S S S #> # ℹ 2,990 more rows # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://amr-for-r.org/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"Conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 24 Jun 2024. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLEPNE\") #> Class 'mo' #> [1] Line truncated
[{"path":"https://amr-for-r.org/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) reliable data thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"Conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://amr-for-r.org/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"Conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #> patient_id hospital date bacteria AMX AMC CIP GEN #> <chr> <chr> <date> <chr> <chr> <chr> <chr> <chr> #> 1 J3 A 2012-11-21 E. coli R I S S #> 2 R7 A 2018-04-03 K. pneumoniae R I S S #> 3 P3 A 2014-09-19 E. coli R S S S #> 4 P10 A 2015-12-10 E. coli S I S S #> 5 B7 A 2015-03-02 E. coli S S S S #> 6 W3 A 2018-03-31 S. aureus R S R S #> 7 J8 A 2016-06-14 E. coli R S S S #> 8 M3 A 2015-10-25 E. coli R S S S #> 9 J3 A 2019-06-19 E. coli S S S S #> 10 G6 A 2015-04-27 S. aureus S S S S #> # ℹ 2,990 more rows # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://amr-for-r.org/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"Conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 24 Jun 2024. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLEPNE\") #> Class 'mo' #> [1] Line truncated