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@ -30,7 +30,7 @@
<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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@ -95,7 +95,7 @@
website update since they are based on randomly created values and the 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 page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was Markdown</a>. However, the methodology remains unchanged. This page was
generated on 22 September 2024.</p> generated on 24 September 2024.</p>
<div class="section level2"> <div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2> </h2>
@ -151,21 +151,21 @@ make the structure of your data generally look like this:</p>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="center">2024-09-22</td> <td align="center">2024-09-24</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">S</td> <td align="center">S</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="center">2024-09-22</td> <td align="center">2024-09-24</td>
<td align="center">abcd</td> <td align="center">abcd</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">S</td> <td align="center">S</td>
<td align="center">R</td> <td align="center">R</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="center">2024-09-22</td> <td align="center">2024-09-24</td>
<td align="center">efgh</td> <td align="center">efgh</td>
<td align="center">Escherichia coli</td> <td align="center">Escherichia coli</td>
<td align="center">R</td> <td align="center">R</td>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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@ -84,7 +84,7 @@
<main id="main" class="col-md-9"><div class="page-header"> <main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1> <img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">22 September 2024</h4> <h4 data-toc-skip class="date">24 September 2024</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> <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> <div class="d-none name"><code>datasets.Rmd</code></div>

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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -29,7 +29,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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@ -32,7 +32,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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@ -92,7 +92,7 @@
<li>Generates <strong>antibiograms</strong> - traditional, combined, syndromic, and even WISCA</li> <li>Generates <strong>antibiograms</strong> - traditional, combined, syndromic, and even WISCA</li>
<li>Provides the <strong>full microbiological taxonomy</strong> and extensive info on <strong>all antimicrobial drugs</strong> <li>Provides the <strong>full microbiological taxonomy</strong> and extensive info on <strong>all antimicrobial drugs</strong>
</li> </li>
<li>Applies all recent <strong>CLSI</strong> and <strong>EUCAST</strong> clinical and veterinary breakpoints for MICs and disk zones</li> <li>Applies all recent <strong>CLSI</strong> and <strong>EUCAST</strong> clinical and veterinary breakpoints for MICs, disk zones and ECOFFs</li>
<li>Corrects for duplicate isolates, <strong>calculates</strong> and <strong>predicts</strong> AMR per antibiotic class</li> <li>Corrects for duplicate isolates, <strong>calculates</strong> and <strong>predicts</strong> AMR per antibiotic class</li>
<li>Integrates with <strong>WHONET</strong>, ATC, <strong>EARS-Net</strong>, PubChem, <strong>LOINC</strong>, <strong>SNOMED CT</strong>, and <strong>NCBI</strong> <li>Integrates with <strong>WHONET</strong>, ATC, <strong>EARS-Net</strong>, PubChem, <strong>LOINC</strong>, <strong>SNOMED CT</strong>, and <strong>NCBI</strong>
</li> </li>
@ -267,115 +267,115 @@
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span> <code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
<span> antibiotics <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="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <span> antibiotics <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="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<table class="table"> <table style="width:100%;" class="table">
<colgroup>
<col width="18%">
<col width="13%">
<col width="12%">
<col width="13%">
<col width="13%">
<col width="13%">
<col width="13%">
</colgroup>
<thead><tr class="header"> <thead><tr class="header">
<th align="left">Pathogen (N min-max)</th> <th align="left">Pathogen</th>
<th align="right">AMK</th> <th align="center">Amikacin</th>
<th align="right">GEN</th> <th align="center">Gentamicin</th>
<th align="right">IPM</th> <th align="center">Imipenem</th>
<th align="right">KAN</th> <th align="center">Kanamycin</th>
<th align="right">MEM</th> <th align="center">Meropenem</th>
<th align="right">TOB</th> <th align="center">Tobramycin</th>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">CoNS (43-309)</td> <td align="left">CoNS</td>
<td align="right">0</td> <td align="center">0% (0/43)</td>
<td align="right">86</td> <td align="center">86% (267/309)</td>
<td align="right">52</td> <td align="center">52% (25/48)</td>
<td align="right">0</td> <td align="center">0% (0/43)</td>
<td align="right">52</td> <td align="center">52% (25/48)</td>
<td align="right">22</td> <td align="center">22% (12/55)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"> <td align="left"><em>E. coli</em></td>
<em>E. coli</em> (0-462)</td> <td align="center">100% (171/171)</td>
<td align="right">100</td> <td align="center">98% (451/460)</td>
<td align="right">98</td> <td align="center">100% (422/422)</td>
<td align="right">100</td> <td align="center"></td>
<td align="right"></td> <td align="center">100% (418/418)</td>
<td align="right">100</td> <td align="center">97% (450/462)</td>
<td align="right">97</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left"> <td align="left"><em>E. faecalis</em></td>
<em>E. faecalis</em> (0-39)</td> <td align="center">0% (0/39)</td>
<td align="right">0</td> <td align="center">0% (0/39)</td>
<td align="right">0</td> <td align="center">100% (38/38)</td>
<td align="right">100</td> <td align="center">0% (0/39)</td>
<td align="right">0</td> <td align="center"></td>
<td align="right"></td> <td align="center">0% (0/39)</td>
<td align="right">0</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"> <td align="left"><em>K. pneumoniae</em></td>
<em>K. pneumoniae</em> (0-58)</td> <td align="center"></td>
<td align="right"></td> <td align="center">90% (52/58)</td>
<td align="right">90</td> <td align="center">100% (51/51)</td>
<td align="right">100</td> <td align="center"></td>
<td align="right"></td> <td align="center">100% (53/53)</td>
<td align="right">100</td> <td align="center">90% (52/58)</td>
<td align="right">90</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left"> <td align="left"><em>P. aeruginosa</em></td>
<em>P. aeruginosa</em> (17-30)</td> <td align="center"></td>
<td align="right"></td> <td align="center">100% (30/30)</td>
<td align="right">100</td> <td align="center"></td>
<td align="right"></td> <td align="center">0% (0/30)</td>
<td align="right">0</td> <td align="center"></td>
<td align="right"></td> <td align="center">100% (30/30)</td>
<td align="right">100</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"> <td align="left"><em>P. mirabilis</em></td>
<em>P. mirabilis</em> (0-34)</td> <td align="center"></td>
<td align="right"></td> <td align="center">94% (32/34)</td>
<td align="right">94</td> <td align="center">94% (30/32)</td>
<td align="right">94</td> <td align="center"></td>
<td align="right"></td> <td align="center"></td>
<td align="right"></td> <td align="center">94% (32/34)</td>
<td align="right">94</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left"> <td align="left"><em>S. aureus</em></td>
<em>S. aureus</em> (2-233)</td> <td align="center"></td>
<td align="right"></td> <td align="center">99% (231/233)</td>
<td align="right">99</td> <td align="center"></td>
<td align="right"></td> <td align="center"></td>
<td align="right"></td> <td align="center"></td>
<td align="right"></td> <td align="center">98% (84/86)</td>
<td align="right">98</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"> <td align="left"><em>S. epidermidis</em></td>
<em>S. epidermidis</em> (8-163)</td> <td align="center">0% (0/44)</td>
<td align="right">0</td> <td align="center">79% (128/163)</td>
<td align="right">79</td> <td align="center"></td>
<td align="right"></td> <td align="center">0% (0/44)</td>
<td align="right">0</td> <td align="center"></td>
<td align="right"></td> <td align="center">51% (45/89)</td>
<td align="right">51</td>
</tr> </tr>
<tr class="odd"> <tr class="odd">
<td align="left"> <td align="left"><em>S. hominis</em></td>
<em>S. hominis</em> (3-80)</td> <td align="center"></td>
<td align="right"></td> <td align="center">92% (74/80)</td>
<td align="right">92</td> <td align="center"></td>
<td align="right"></td> <td align="center"></td>
<td align="right"></td> <td align="center"></td>
<td align="right"></td> <td align="center">85% (53/62)</td>
<td align="right">85</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left"> <td align="left"><em>S. pneumoniae</em></td>
<em>S. pneumoniae</em> (11-117)</td> <td align="center">0% (0/117)</td>
<td align="right">0</td> <td align="center">0% (0/117)</td>
<td align="right">0</td> <td align="center"></td>
<td align="right"></td> <td align="center">0% (0/117)</td>
<td align="right">0</td> <td align="center"></td>
<td align="right"></td> <td align="center">0% (0/117)</td>
<td align="right">0</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@ -385,24 +385,30 @@
<span> antibiotics <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">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span> <span> antibiotics <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">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></code></pre></div> <span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></code></pre></div>
<table class="table"> <table class="table">
<colgroup>
<col width="12%">
<col width="21%">
<col width="33%">
<col width="32%">
</colgroup>
<thead><tr class="header"> <thead><tr class="header">
<th align="left">Pathogen (N min-max)</th> <th align="left">Pathogen</th>
<th align="right">TZP</th> <th align="center">Piperacillin/tazobactam</th>
<th align="right">TZP + GEN</th> <th align="center">Piperacillin/tazobactam + Gentamicin</th>
<th align="right">TZP + TOB</th> <th align="center">Piperacillin/tazobactam + Tobramycin</th>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">Gram-negative (641-693)</td> <td align="left">Gram-negative</td>
<td align="right">88</td> <td align="center">88% (565/641)</td>
<td align="right">99</td> <td align="center">99% (681/691)</td>
<td align="right">98</td> <td align="center">98% (679/693)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Gram-positive (345-1044)</td> <td align="left">Gram-positive</td>
<td align="right">86</td> <td align="center">86% (296/345)</td>
<td align="right">98</td> <td align="center">98% (1018/1044)</td>
<td align="right">95</td> <td align="center">95% (524/550)</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>
@ -414,24 +420,30 @@
<span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span> <span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
<span> language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span></code></pre></div> <span> language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span></code></pre></div>
<table class="table"> <table class="table">
<colgroup>
<col width="20%">
<col width="27%">
<col width="26%">
<col width="25%">
</colgroup>
<thead><tr class="header"> <thead><tr class="header">
<th align="left">Збудник (N min-max)</th> <th align="left">Збудник</th>
<th align="right">Гентаміцин</th> <th align="center">Гентаміцин</th>
<th align="right">Тобраміцин</th> <th align="center">Тобраміцин</th>
<th align="right">Ципрофлоксацин</th> <th align="center">Ципрофлоксацин</th>
</tr></thead> </tr></thead>
<tbody> <tbody>
<tr class="odd"> <tr class="odd">
<td align="left">Грамнегативні (684-686)</td> <td align="left">Грамнегативні</td>
<td align="right">96</td> <td align="center">96% (659/684)</td>
<td align="right">96</td> <td align="center">96% (658/686)</td>
<td align="right">91</td> <td align="center">91% (621/684)</td>
</tr> </tr>
<tr class="even"> <tr class="even">
<td align="left">Грампозитивні (665-1170)</td> <td align="left">Грампозитивні</td>
<td align="right">63</td> <td align="center">63% (740/1170)</td>
<td align="right">34</td> <td align="center">34% (228/665)</td>
<td align="right">77</td> <td align="center">77% (560/724)</td>
</tr> </tr>
</tbody> </tbody>
</table> </table>

27
news/index.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -53,18 +53,18 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1.9078" id="amr-2119078">AMR 2.1.1.9078<a class="anchor" aria-label="anchor" href="#amr-2119078"></a></h2> <h2 class="pkg-version" data-toc-text="2.1.1.9080" id="amr-2119080">AMR 2.1.1.9080<a class="anchor" aria-label="anchor" href="#amr-2119080"></a></h2>
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p> <p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
<div class="section level5"> <div class="section level5">
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9078">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9078"></a></h5> <h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9080">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9080"></a></h5>
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p> <p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
</div> </div>
<div class="section level3"> <div class="section level3">
<h3 id="breaking-2-1-1-9078">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9078"></a></h3> <h3 id="breaking-2-1-1-9080">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9080"></a></h3>
<ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over a year ago</li> <ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over a year ago</li>
</ul></div> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="new-2-1-1-9078">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9078"></a></h3> <h3 id="new-2-1-1-9080">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9080"></a></h3>
<ul><li>One Health implementation <ul><li>One Health implementation
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for animal breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li> <ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for animal breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
<li>The <code>clinical_breakpoints</code> data set contains all these breakpoints, and can be downloaded on our <a href="https://msberends.github.io/AMR/articles/datasets.html">download page</a>.</li> <li>The <code>clinical_breakpoints</code> data set contains all these breakpoints, and can be downloaded on our <a href="https://msberends.github.io/AMR/articles/datasets.html">download page</a>.</li>
@ -101,7 +101,7 @@
</ul></li> </ul></li>
</ul></div> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="changed-2-1-1-9078">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9078"></a></h3> <h3 id="changed-2-1-1-9080">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9080"></a></h3>
<ul><li>SIR interpretation <ul><li>SIR interpretation
<ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li> <ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li> <li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
@ -147,24 +147,11 @@
<li>Fixed a bug for when <code><a href="../reference/antibiogram.html">antibiogram()</a></code> returns an empty data set</li> <li>Fixed a bug for when <code><a href="../reference/antibiogram.html">antibiogram()</a></code> returns an empty data set</li>
</ul></div> </ul></div>
<div class="section level3"> <div class="section level3">
<h3 id="other-2-1-1-9078">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9078"></a></h3> <h3 id="other-2-1-1-9080">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9080"></a></h3>
<ul><li>Greatly updated and expanded documentation</li> <ul><li>Greatly updated and expanded documentation</li>
<li>Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li> <li>Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
</ul></div> </ul></div>
</div> </div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="2.1.1" id="amr-211">AMR 2.1.1<a class="anchor" aria-label="anchor" href="#amr-211"></a></h2><p class="text-muted">CRAN release: 2023-10-21</p>
<ul><li>Fix for selecting first isolates using the phenotype-based method
<ul><li>This included too many isolates when patients had altering antibiograms within the same bacterial species</li>
<li>See for more info <a href="https://github.com/msberends/AMR/issues/122" class="external-link">our issue </a><a href="https://github.com/msberends/AMR/issues/122" class="external-link">#122</a>
</li>
</ul></li>
<li>Added 1,366 LOINC codes to the <code>antibiotics</code> data set and updated to the latest version (LOINC v2.76)</li>
<li>MICs can now be used in complex number calculations and allow scientific number format as input (e.g., <code>as.mic("1.28e-2")</code>)</li>
<li>Fix rounding MICs on latest R beta (‘R-devel’)</li>
<li>Removed unneeded note about the used language when option <code>AMR_locale</code> is set</li>
<li>Fixed non-ASCII characters in documentation, according to CRAN maintainers</li>
</ul><hr></div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
</nav></aside></div> </nav></aside></div>

2
pkgdown.yml
View File

@ -11,7 +11,7 @@ articles:
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
WHONET: WHONET.html WHONET: WHONET.html
last_built: 2024-09-22T09:52Z last_built: 2024-09-24T20:45Z
urls: urls:
reference: https://msberends.github.io/AMR/reference reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles article: https://msberends.github.io/AMR/articles

2
reference/AMR-options.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/AMR.html
View File

@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/WHOCC.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/WHONET.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/ab_from_text.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
reference/ab_property.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -105,7 +105,7 @@
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt> <dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
<dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd> <dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the package option <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt id="arg-tolower">tolower<a class="anchor" aria-label="anchor" href="#arg-tolower"></a></dt> <dt id="arg-tolower">tolower<a class="anchor" aria-label="anchor" href="#arg-tolower"></a></dt>

6
reference/add_custom_antimicrobials.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -76,8 +76,8 @@
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p><strong>Important:</strong> Due to how <span style="R">R</span> works, the <code>add_custom_antimicrobials()</code> function has to be run in every <span style="R">R</span> session - added antimicrobials are not stored between sessions and are thus lost when <span style="R">R</span> is exited.</p> <p><strong>Important:</strong> Due to how <span style="R">R</span> works, the <code>add_custom_antimicrobials()</code> function has to be run in every <span style="R">R</span> session - added antimicrobials are not stored between sessions and are thus lost when <span style="R">R</span> is exited.</p>
<p>There are two ways to circumvent this and automate the process of adding antimicrobials:</p> <p>There are two ways to circumvent this and automate the process of adding antimicrobials:</p>
<p><strong>Method 1:</strong> Using the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_custom_ab</a></code>, which is the preferred method. To use this method:</p><ol><li><p>Create a data set in the structure of the <a href="antibiotics.html">antibiotics</a> data set (containing at the very least columns "ab" and "name") and save it with <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> to a location of choice, e.g. <code>"~/my_custom_ab.rds"</code>, or any remote location.</p></li> <p><strong>Method 1:</strong> Using the package option <code><a href="AMR-options.html">AMR_custom_ab</a></code>, which is the preferred method. To use this method:</p><ol><li><p>Create a data set in the structure of the <a href="antibiotics.html">antibiotics</a> data set (containing at the very least columns "ab" and "name") and save it with <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> to a location of choice, e.g. <code>"~/my_custom_ab.rds"</code>, or any remote location.</p></li>
<li><p>Set the file location to the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_custom_ab</a></code>: <code>options(AMR_custom_ab = "~/my_custom_ab.rds")</code>. This can even be a remote file location, such as an https URL. Since options are not saved between <span style="R">R</span> sessions, it is best to save this option to the <code>.Rprofile</code> file so that it will be loaded on start-up of <span style="R">R</span>. To do this, open the <code>.Rprofile</code> file using e.g. <code>utils::file.edit("~/.Rprofile")</code>, add this text and save the file:</p> <li><p>Set the file location to the package option <code><a href="AMR-options.html">AMR_custom_ab</a></code>: <code>options(AMR_custom_ab = "~/my_custom_ab.rds")</code>. This can even be a remote file location, such as an https URL. Since options are not saved between <span style="R">R</span> sessions, it is best to save this option to the <code>.Rprofile</code> file so that it will be loaded on start-up of <span style="R">R</span>. To do this, open the <code>.Rprofile</code> file using e.g. <code>utils::file.edit("~/.Rprofile")</code>, add this text and save the file:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="co"># Add custom antimicrobial codes:</span></span> <p></p><div class="sourceCode r"><pre><code><span><span class="co"># Add custom antimicrobial codes:</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_custom_ab <span class="op">=</span> <span class="st">"~/my_custom_ab.rds"</span><span class="op">)</span></span></code></pre><p></p></div> <span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_custom_ab <span class="op">=</span> <span class="st">"~/my_custom_ab.rds"</span><span class="op">)</span></span></code></pre><p></p></div>
<p>Upon package load, this file will be loaded and run through the <code>add_custom_antimicrobials()</code> function.</p></li> <p>Upon package load, this file will be loaded and run through the <code>add_custom_antimicrobials()</code> function.</p></li>

6
reference/add_custom_microorganisms.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -77,8 +77,8 @@
<p>This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see <em>Examples</em>.</p> <p>This function will fill in missing taxonomy for you, if specific taxonomic columns are missing, see <em>Examples</em>.</p>
<p><strong>Important:</strong> Due to how <span style="R">R</span> works, the <code>add_custom_microorganisms()</code> function has to be run in every <span style="R">R</span> session - added microorganisms are not stored between sessions and are thus lost when <span style="R">R</span> is exited.</p> <p><strong>Important:</strong> Due to how <span style="R">R</span> works, the <code>add_custom_microorganisms()</code> function has to be run in every <span style="R">R</span> session - added microorganisms are not stored between sessions and are thus lost when <span style="R">R</span> is exited.</p>
<p>There are two ways to circumvent this and automate the process of adding microorganisms:</p> <p>There are two ways to circumvent this and automate the process of adding microorganisms:</p>
<p><strong>Method 1:</strong> Using the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_custom_mo</a></code>, which is the preferred method. To use this method:</p><ol><li><p>Create a data set in the structure of the <a href="microorganisms.html">microorganisms</a> data set (containing at the very least column "genus") and save it with <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> to a location of choice, e.g. <code>"~/my_custom_mo.rds"</code>, or any remote location.</p></li> <p><strong>Method 1:</strong> Using the package option <code><a href="AMR-options.html">AMR_custom_mo</a></code>, which is the preferred method. To use this method:</p><ol><li><p>Create a data set in the structure of the <a href="microorganisms.html">microorganisms</a> data set (containing at the very least column "genus") and save it with <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS()</a></code> to a location of choice, e.g. <code>"~/my_custom_mo.rds"</code>, or any remote location.</p></li>
<li><p>Set the file location to the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_custom_mo</a></code>: <code>options(AMR_custom_mo = "~/my_custom_mo.rds")</code>. This can even be a remote file location, such as an https URL. Since options are not saved between <span style="R">R</span> sessions, it is best to save this option to the <code>.Rprofile</code> file so that it will be loaded on start-up of <span style="R">R</span>. To do this, open the <code>.Rprofile</code> file using e.g. <code>utils::file.edit("~/.Rprofile")</code>, add this text and save the file:</p> <li><p>Set the file location to the package option <code><a href="AMR-options.html">AMR_custom_mo</a></code>: <code>options(AMR_custom_mo = "~/my_custom_mo.rds")</code>. This can even be a remote file location, such as an https URL. Since options are not saved between <span style="R">R</span> sessions, it is best to save this option to the <code>.Rprofile</code> file so that it will be loaded on start-up of <span style="R">R</span>. To do this, open the <code>.Rprofile</code> file using e.g. <code>utils::file.edit("~/.Rprofile")</code>, add this text and save the file:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="co"># Add custom microorganism codes:</span></span> <p></p><div class="sourceCode r"><pre><code><span><span class="co"># Add custom microorganism codes:</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_custom_mo <span class="op">=</span> <span class="st">"~/my_custom_mo.rds"</span><span class="op">)</span></span></code></pre><p></p></div> <span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>AMR_custom_mo <span class="op">=</span> <span class="st">"~/my_custom_mo.rds"</span><span class="op">)</span></span></code></pre><p></p></div>
<p>Upon package load, this file will be loaded and run through the <code>add_custom_microorganisms()</code> function.</p></li> <p>Upon package load, this file will be loaded and run through the <code>add_custom_microorganisms()</code> function.</p></li>

22
reference/age.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -116,16 +116,16 @@
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</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> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.79781 34</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.80328 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.56011 19</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.56557 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.89071 50</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.89617 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.60383 52</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.60929 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.59016 59</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.59563 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.69945 11</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.70492 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 27 27.07104 2</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 27 27.07650 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.65574 21</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.66120 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.26503 27</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.27049 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 38 38.11749 13</span> <span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 38 38.12295 13</span>
</code></pre></div> </code></pre></div>
</div> </div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

2
reference/age_groups.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

6
reference/antibiogram.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -117,7 +117,7 @@
<dt id="arg-ab-transform">ab_transform<a class="anchor" aria-label="anchor" href="#arg-ab-transform"></a></dt> <dt id="arg-ab-transform">ab_transform<a class="anchor" aria-label="anchor" href="#arg-ab-transform"></a></dt>
<dd><p>a character to transform antibiotic input - must be one of the column names of the <a href="antibiotics.html">antibiotics</a> data set (defaults to "name"): "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be <code>NULL</code> to not transform the input.</p></dd> <dd><p>a character to transform antibiotic input - must be one of the column names of the <a href="antibiotics.html">antibiotics</a> data set (defaults to <code>"name"</code>): "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be <code>NULL</code> to not transform the input.</p></dd>
<dt id="arg-syndromic-group">syndromic_group<a class="anchor" aria-label="anchor" href="#arg-syndromic-group"></a></dt> <dt id="arg-syndromic-group">syndromic_group<a class="anchor" aria-label="anchor" href="#arg-syndromic-group"></a></dt>
@ -199,7 +199,7 @@
<li><p>5% (15/300)</p></li> <li><p>5% (15/300)</p></li>
<li><p>5 (N=15/300)</p></li> <li><p>5 (N=15/300)</p></li>
<li><p>5% (N=15/300)</p></li> <li><p>5% (N=15/300)</p></li>
</ol><p>The default is <code>10</code>, which can be set globally with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_antibiogram_formatting_type</a></code>, e.g. <code>options(AMR_antibiogram_formatting_type = 5)</code>.</p> </ol><p>The default is <code>10</code>, which can be set globally with the package option <code><a href="AMR-options.html">AMR_antibiogram_formatting_type</a></code>, e.g. <code>options(AMR_antibiogram_formatting_type = 5)</code>.</p>
<p>Set <code>digits</code> (defaults to <code>0</code>) to alter the rounding of the susceptibility percentage.</p> <p>Set <code>digits</code> (defaults to <code>0</code>) to alter the rounding of the susceptibility percentage.</p>
</div> </div>

2
reference/antibiotic_class_selectors.html
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@ -9,7 +9,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/antibiotics.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/as.ab.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/as.av.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/as.disk.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/as.mic.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

10
reference/as.mo.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -110,7 +110,7 @@
<dt id="arg-keep-synonyms">keep_synonyms<a class="anchor" aria-label="anchor" href="#arg-keep-synonyms"></a></dt> <dt id="arg-keep-synonyms">keep_synonyms<a class="anchor" aria-label="anchor" href="#arg-keep-synonyms"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is <code>FALSE</code>, which will return a note if old taxonomic names were processed. The default can be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_keep_synonyms</a></code>, i.e. <code>options(AMR_keep_synonyms = TRUE)</code> or <code>options(AMR_keep_synonyms = FALSE)</code>.</p></dd> <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is <code>FALSE</code>, which will return a note if old taxonomic names were processed. The default can be set with the package option <code><a href="AMR-options.html">AMR_keep_synonyms</a></code>, i.e. <code>options(AMR_keep_synonyms = TRUE)</code> or <code>options(AMR_keep_synonyms = FALSE)</code>.</p></dd>
<dt id="arg-reference-df">reference_df<a class="anchor" aria-label="anchor" href="#arg-reference-df"></a></dt> <dt id="arg-reference-df">reference_df<a class="anchor" aria-label="anchor" href="#arg-reference-df"></a></dt>
@ -118,15 +118,15 @@
<dt id="arg-ignore-pattern">ignore_pattern<a class="anchor" aria-label="anchor" href="#arg-ignore-pattern"></a></dt> <dt id="arg-ignore-pattern">ignore_pattern<a class="anchor" aria-label="anchor" href="#arg-ignore-pattern"></a></dt>
<dd><p>a Perl-compatible <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) of which all matches in <code>x</code> must return <code>NA</code>. This can be convenient to exclude known non-relevant input and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_ignore_pattern</a></code>, e.g. <code>options(AMR_ignore_pattern = "(not reported|contaminated flora)")</code>.</p></dd> <dd><p>a Perl-compatible <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) of which all matches in <code>x</code> must return <code>NA</code>. This can be convenient to exclude known non-relevant input and can also be set with the package option <code><a href="AMR-options.html">AMR_ignore_pattern</a></code>, e.g. <code>options(AMR_ignore_pattern = "(not reported|contaminated flora)")</code>.</p></dd>
<dt id="arg-cleaning-regex">cleaning_regex<a class="anchor" aria-label="anchor" href="#arg-cleaning-regex"></a></dt> <dt id="arg-cleaning-regex">cleaning_regex<a class="anchor" aria-label="anchor" href="#arg-cleaning-regex"></a></dt>
<dd><p>a Perl-compatible <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) to clean the input of <code>x</code>. Every matched part in <code>x</code> will be removed. At default, this is the outcome of <code>mo_cleaning_regex()</code>, which removes texts between brackets and texts such as "species" and "serovar". The default can be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_cleaning_regex</a></code>.</p></dd> <dd><p>a Perl-compatible <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) to clean the input of <code>x</code>. Every matched part in <code>x</code> will be removed. At default, this is the outcome of <code>mo_cleaning_regex()</code>, which removes texts between brackets and texts such as "species" and "serovar". The default can be set with the package option <code><a href="AMR-options.html">AMR_cleaning_regex</a></code>.</p></dd>
<dt id="arg-only-fungi">only_fungi<a class="anchor" aria-label="anchor" href="#arg-only-fungi"></a></dt> <dt id="arg-only-fungi">only_fungi<a class="anchor" aria-label="anchor" href="#arg-only-fungi"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if only fungi must be found, making sure that e.g. misspellings always return records from the kingdom of Fungi. This can be set globally for <a href="mo_property.html">all microorganism functions</a> with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_only_fungi</a></code>, i.e. <code>options(AMR_only_fungi = TRUE)</code>.</p></dd> <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if only fungi must be found, making sure that e.g. misspellings always return records from the kingdom of Fungi. This can be set globally for <a href="mo_property.html">all microorganism functions</a> with the package option <code><a href="AMR-options.html">AMR_only_fungi</a></code>, i.e. <code>options(AMR_only_fungi = TRUE)</code>.</p></dd>
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt> <dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>

78
reference/as.sir.html
View File

@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -189,7 +189,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt> <dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt>
<dd><p>defaults to EUCAST 2024 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2011-2024) and CLSI (2011-2024), see <em>Details</em>.</p></dd> <dd><p>defaults to EUCAST 2024 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the package option <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2011-2024) and CLSI (2011-2024), see <em>Details</em>.</p></dd>
<dt id="arg-uti">uti<a class="anchor" aria-label="anchor" href="#arg-uti"></a></dt> <dt id="arg-uti">uti<a class="anchor" aria-label="anchor" href="#arg-uti"></a></dt>
@ -209,15 +209,15 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<dt id="arg-include-screening">include_screening<a class="anchor" aria-label="anchor" href="#arg-include-screening"></a></dt> <dt id="arg-include-screening">include_screening<a class="anchor" aria-label="anchor" href="#arg-include-screening"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that clinical breakpoints for screening are allowed - the default is <code>FALSE</code>. Can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_include_screening</a></code>.</p></dd> <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that clinical breakpoints for screening are allowed - the default is <code>FALSE</code>. Can also be set with the package option <code><a href="AMR-options.html">AMR_include_screening</a></code>.</p></dd>
<dt id="arg-include-pkpd">include_PKPD<a class="anchor" aria-label="anchor" href="#arg-include-pkpd"></a></dt> <dt id="arg-include-pkpd">include_PKPD<a class="anchor" aria-label="anchor" href="#arg-include-pkpd"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is <code>TRUE</code>. Can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_include_PKPD</a></code>.</p></dd> <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is <code>TRUE</code>. Can also be set with the package option <code><a href="AMR-options.html">AMR_include_PKPD</a></code>.</p></dd>
<dt id="arg-breakpoint-type">breakpoint_type<a class="anchor" aria-label="anchor" href="#arg-breakpoint-type"></a></dt> <dt id="arg-breakpoint-type">breakpoint_type<a class="anchor" aria-label="anchor" href="#arg-breakpoint-type"></a></dt>
<dd><p>the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is <code>"human"</code>, which can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>. If <code>host</code> is set to values of veterinary species, this will automatically be set to <code>"animal"</code>.</p></dd> <dd><p>the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is <code>"human"</code>, which can also be set with the package option <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>. If <code>host</code> is set to values of veterinary species, this will automatically be set to <code>"animal"</code>.</p></dd>
<dt id="arg-host">host<a class="anchor" aria-label="anchor" href="#arg-host"></a></dt> <dt id="arg-host">host<a class="anchor" aria-label="anchor" href="#arg-host"></a></dt>
@ -276,7 +276,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are for <strong>clinical microbiology</strong>: EUCAST 2011-2024 and CLSI 2011-2024, and for <strong>veterinary microbiology</strong>: EUCAST 2021-2024 and CLSI 2019-2024.</p> <p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are for <strong>clinical microbiology</strong>: EUCAST 2011-2024 and CLSI 2011-2024, and for <strong>veterinary microbiology</strong>: EUCAST 2021-2024 and CLSI 2019-2024.</p>
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2024"</code> or <code>"CLSI 2024"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p> <p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2024"</code> or <code>"CLSI 2024"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
<p>You can set the default guideline with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code> (e.g. in your <code>.Rprofile</code> file), such as:</p> <p>You can set the default guideline with the package option <code><a href="AMR-options.html">AMR_guideline</a></code> (e.g. in your <code>.Rprofile</code> file), such as:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI"</span>)</span> <p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI"</span>)</span>
<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI 2018"</span>)</span> <span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI 2018"</span>)</span>
<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"EUCAST 2020"</span>)</span> <span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a> <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"EUCAST 2020"</span>)</span>
@ -568,7 +568,8 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'amoxicillin' (AMX) based on column</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'amoxicillin' (AMX) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
@ -578,23 +579,27 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'amoxicillin' (AMX) based on column</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'amoxicillin' (AMX) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> column 'microorganism', EUCAST 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> column 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin) based on</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'genta' (GEN, gentamicin) based on</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> column 'microorganism', EUCAST 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> column 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'amoxicillin' (AMX) based on column</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'amoxicillin' (AMX) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
@ -604,27 +609,31 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'amoxicillin' (AMX) based on column</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'amoxicillin' (AMX) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> column 'microorganism', EUCAST 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> column 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'amoxicillin' (AMX) based on column</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'amoxicillin' (AMX) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: 'cipro' (CIP, ciprofloxacin) based on column</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: 'tobra' (TOB, tobramycin) based on</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> column 'microorganism', EUCAST 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> column 'microorganism', EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
@ -726,8 +735,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'nitrofuratoin' (NIT, nitrofurantoin),</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'nitrofuratoin' (NIT, nitrofurantoin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for nitrofurantoin (NIT) in Escherichia coli are only available for (uncomplicated) urinary tract infections (UTI); assuming uti = TRUE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> infection.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> infection.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Use as.sir(uti = FALSE) to prevent this.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Use as.sir(uti = FALSE) to prevent this.</span>
@ -736,8 +744,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'nitrofuratoin' (NIT, nitrofurantoin),</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'nitrofuratoin' (NIT, nitrofurantoin),</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for nitrofurantoin (NIT) in Escherichia coli are only available for (uncomplicated) urinary tract infections (UTI); assuming uti = TRUE.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
@ -760,17 +767,20 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'amoxicillin' (AMX), EUCAST 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'amoxicillin' (AMX), EUCAST 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for amoxicillin (AMX) in Escherichia coli - assuming body site 'Intravenous'. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'cipro' (CIP, ciprofloxacin), EUCAST</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column 'cipro' (CIP, ciprofloxacin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'tobra' (TOB, tobramycin), EUCAST</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'tobra' (TOB, tobramycin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'genta' (GEN, gentamicin), EUCAST</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting disk diffusion zones: column 'genta' (GEN, gentamicin), EUCAST</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 2024...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> 2024...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in Escherichia coli - assuming an unspecified body site. Use argument uti to set which isolates are from urine. See ?as.sir.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Assigning class 'sir' to already clean column 'ERY' (erythromycin)...</span> <span class="r-msg co"><span class="r-pr">#&gt;</span> Assigning class 'sir' to already clean column 'ERY' (erythromycin)...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span> <span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> microorganism amoxicillin cipro tobra genta ERY</span> <span class="r-out co"><span class="r-pr">#&gt;</span> microorganism amoxicillin cipro tobra genta ERY</span>
@ -778,20 +788,20 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span></span></span> <span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># return a 'logbook' about the results:</span></span></span> <span class="r-in"><span><span class="co"># return a 'logbook' about the results:</span></span></span>
<span class="r-in"><span><span class="fu">sir_interpretation_history</span><span class="op">(</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">sir_interpretation_history</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 59 × 16</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 57 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_given mo_given host_given ab mo </span> <span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_given mo_given host_given ab mo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</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;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</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;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-09-22 <span style="color: #949494;">09:53:01</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-09-24 <span style="color: #949494;">20:46:27</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-09-22 <span style="color: #949494;">09:53:08</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-09-24 <span style="color: #949494;">20:46:34</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-09-22 <span style="color: #949494;">09:53:08</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-09-24 <span style="color: #949494;">20:46:34</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-09-22 <span style="color: #949494;">09:53:09</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-09-24 <span style="color: #949494;">20:46:35</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-09-22 <span style="color: #949494;">09:53:09</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-09-24 <span style="color: #949494;">20:46:35</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-09-22 <span style="color: #949494;">09:53:01</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-09-24 <span style="color: #949494;">20:46:27</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-09-22 <span style="color: #949494;">09:53:08</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-09-24 <span style="color: #949494;">20:46:34</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-09-22 <span style="color: #949494;">09:53:08</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-09-24 <span style="color: #949494;">20:46:34</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-09-22 <span style="color: #949494;">09:53:09</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-09-24 <span style="color: #949494;">20:46:35</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-09-22 <span style="color: #949494;">09:53:09</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-09-24 <span style="color: #949494;">20:46:35</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 49 more rows</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;dbl&gt;, outcome &lt;sir&gt;,</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;dbl&gt;, outcome &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># 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;"># 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;</span></span> <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;</span></span>

2
reference/atc_online.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/av_from_text.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
reference/av_property.html
View File

@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -93,7 +93,7 @@
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt> <dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
<dd><p>language of the returned text - the default is system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd> <dd><p>language of the returned text - the default is system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the package option <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt id="arg-tolower">tolower<a class="anchor" aria-label="anchor" href="#arg-tolower"></a></dt> <dt id="arg-tolower">tolower<a class="anchor" aria-label="anchor" href="#arg-tolower"></a></dt>

2
reference/availability.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
reference/bug_drug_combinations.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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@ -101,7 +101,7 @@
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt> <dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
<dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd> <dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the package option <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt id="arg-minimum">minimum<a class="anchor" aria-label="anchor" href="#arg-minimum"></a></dt> <dt id="arg-minimum">minimum<a class="anchor" aria-label="anchor" href="#arg-minimum"></a></dt>

27
reference/clinical_breakpoints.html
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@ -1,10 +1,18 @@
<!DOCTYPE html> <!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints"><meta name="description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs. <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints"><meta name="description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.
Currently available breakpoint guidelines for clinical microbiology are EUCAST 2011-2024 and CLSI 2011-2024. These breakpoints are currently implemented:
Currently available breakpoint guidelines for veterinary microbiology are EUCAST 2021-2024 and CLSI 2019-2024. For clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024;
For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2024 and CLSI 2022-2024.
Use as.sir() to transform MICs or disks measurements to SIR values."><meta property="og:description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs. Use as.sir() to transform MICs or disks measurements to SIR values."><meta property="og:description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.
Currently available breakpoint guidelines for clinical microbiology are EUCAST 2011-2024 and CLSI 2011-2024. These breakpoints are currently implemented:
Currently available breakpoint guidelines for veterinary microbiology are EUCAST 2021-2024 and CLSI 2019-2024. For clinical microbiology: EUCAST 2011-2024 and CLSI 2011-2024;
For veterinary microbiology: EUCAST 2021-2024 and CLSI 2019-2024;
For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2024 and CLSI 2022-2024.
Use as.sir() to transform MICs or disks measurements to SIR values."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"></head><body> Use as.sir() to transform MICs or disks measurements to SIR values."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"></head><body>
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@ -13,7 +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> <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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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@ -61,9 +69,10 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<div class="ref-description section level2"> <div class="ref-description section level2">
<p>Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.</p> <p>Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.</p>
<p>Currently available breakpoint guidelines for <strong>clinical microbiology</strong> are EUCAST 2011-2024 and CLSI 2011-2024.</p> <p>These breakpoints are currently implemented:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2024 and CLSI 2011-2024;</p></li>
<p>Currently available breakpoint guidelines for <strong>veterinary microbiology</strong> are EUCAST 2021-2024 and CLSI 2019-2024.</p> <li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2024 and CLSI 2019-2024;</p></li>
<p>Use <code><a href="as.sir.html">as.sir()</a></code> to transform MICs or disks measurements to SIR values.</p> <li><p>For <strong>ECOFFs</strong> (Epidemiological Cut-off Values): EUCAST 2020-2024 and CLSI 2022-2024.</p></li>
</ul><p>Use <code><a href="as.sir.html">as.sir()</a></code> to transform MICs or disks measurements to SIR values.</p>
</div> </div>
<div class="section level2"> <div class="section level2">
@ -96,7 +105,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<p>Supported types of breakpoints are ECOFF, animal, and human. ECOFF (Epidemiological cut-off) values are used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi.</p> <p>Supported types of breakpoints are ECOFF, animal, and human. ECOFF (Epidemiological cut-off) values are used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi.</p>
<p>The default is <code>"human"</code>, which can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>. Use <code><a href="as.sir.html">as.sir(..., breakpoint_type = ...)</a></code> to interpret raw data using a specific breakpoint type, e.g. <code>as.sir(..., breakpoint_type = "ECOFF")</code> to use ECOFFs.</p> <p>The default is <code>"human"</code>, which can also be set with the package option <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>. Use <code><a href="as.sir.html">as.sir(..., breakpoint_type = ...)</a></code> to interpret raw data using a specific breakpoint type, e.g. <code>as.sir(..., breakpoint_type = "ECOFF")</code> to use ECOFFs.</p>
</div> </div>
<div class="section"> <div class="section">

4
reference/count.html
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@ -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> <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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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@ -109,7 +109,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt> <dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
<dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd> <dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the package option <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt> <dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt>

2
reference/custom_eucast_rules.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/dosage.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a> <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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6
reference/eucast_rules.html
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@ -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> <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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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@ -109,7 +109,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dt id="arg-rules">rules<a class="anchor" aria-label="anchor" href="#arg-rules"></a></dt> <dt id="arg-rules">rules<a class="anchor" aria-label="anchor" href="#arg-rules"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expert")</code>. The default value can be set to another value using the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_eucastrules</a></code>: <code>options(AMR_eucastrules = "all")</code>. If using <code>"custom"</code>, be sure to fill in argument <code>custom_rules</code> too. Custom rules can be created with <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>.</p></dd> <dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expert")</code>. The default value can be set to another value using the package option <code><a href="AMR-options.html">AMR_eucastrules</a></code>: <code>options(AMR_eucastrules = "all")</code>. If using <code>"custom"</code>, be sure to fill in argument <code>custom_rules</code> too. Custom rules can be created with <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>.</p></dd>
<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt> <dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
@ -173,7 +173,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:</p><ol><li><p>A drug <strong>with</strong> enzyme inhibitor will be set to S if the same drug <strong>without</strong> enzyme inhibitor is S</p></li> <p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:</p><ol><li><p>A drug <strong>with</strong> enzyme inhibitor will be set to S if the same drug <strong>without</strong> enzyme inhibitor is S</p></li>
<li><p>A drug <strong>without</strong> enzyme inhibitor will be set to R if the same drug <strong>with</strong> enzyme inhibitor is R</p></li> <li><p>A drug <strong>without</strong> enzyme inhibitor will be set to R if the same drug <strong>with</strong> enzyme inhibitor is R</p></li>
</ol><p>Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.</p> </ol><p>Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.</p>
<p>Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include <code>"other"</code> to the <code>rules</code> argument, or use <code>eucast_rules(..., rules = "all")</code>. You can also set the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_eucastrules</a></code>, i.e. run <code>options(AMR_eucastrules = "all")</code>.</p> <p>Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include <code>"other"</code> to the <code>rules</code> argument, or use <code>eucast_rules(..., rules = "all")</code>. You can also set the package option <code><a href="AMR-options.html">AMR_eucastrules</a></code>, i.e. run <code>options(AMR_eucastrules = "all")</code>.</p>
</div> </div>
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2
reference/example_isolates.html
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@ -7,7 +7,7 @@
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2
reference/example_isolates_unclean.html
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@ -7,7 +7,7 @@
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2
reference/export_ncbi_biosample.html
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@ -7,7 +7,7 @@
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2
reference/first_isolate.html
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@ -9,7 +9,7 @@
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2
reference/g.test.html
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@ -7,7 +7,7 @@
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/get_episode.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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2
reference/ggplot_pca.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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4
reference/ggplot_sir.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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@ -161,7 +161,7 @@
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt> <dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
<dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd> <dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the package option <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt id="arg-nrow">nrow<a class="anchor" aria-label="anchor" href="#arg-nrow"></a></dt> <dt id="arg-nrow">nrow<a class="anchor" aria-label="anchor" href="#arg-nrow"></a></dt>

2
reference/guess_ab_col.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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2
reference/index.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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2
reference/intrinsic_resistant.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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2
reference/italicise_taxonomy.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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2
reference/join.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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2
reference/key_antimicrobials.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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2
reference/kurtosis.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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2
reference/like.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/mdro.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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2
reference/mean_amr_distance.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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2
reference/microorganisms.codes.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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2
reference/microorganisms.groups.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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2
reference/microorganisms.html
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@ -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> <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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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2
reference/mo_matching_score.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</small>
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4
reference/mo_property.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -330,7 +330,7 @@
<dt id="arg-keep-synonyms">keep_synonyms<a class="anchor" aria-label="anchor" href="#arg-keep-synonyms"></a></dt> <dt id="arg-keep-synonyms">keep_synonyms<a class="anchor" aria-label="anchor" href="#arg-keep-synonyms"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is <code>FALSE</code>, which will return a note if old taxonomic names were processed. The default can be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_keep_synonyms</a></code>, i.e. <code>options(AMR_keep_synonyms = TRUE)</code> or <code>options(AMR_keep_synonyms = FALSE)</code>.</p></dd> <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is <code>FALSE</code>, which will return a note if old taxonomic names were processed. The default can be set with the package option <code><a href="AMR-options.html">AMR_keep_synonyms</a></code>, i.e. <code>options(AMR_keep_synonyms = TRUE)</code> or <code>options(AMR_keep_synonyms = FALSE)</code>.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>

4
reference/mo_source.html
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@ -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> <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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -85,7 +85,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<div class="section level2"> <div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an <span style="R">R</span> object file (extension '.rds'). To use an Excel file, you will need to have the <code>readxl</code> package installed.</p> <p>The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an <span style="R">R</span> object file (extension '.rds'). To use an Excel file, you will need to have the <code>readxl</code> package installed.</p>
<p><code>set_mo_source()</code> will check the file for validity: it must be a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, must have a column named <code>"mo"</code> which contains values from <code><a href="microorganisms.html">microorganisms$mo</a></code> or <code><a href="microorganisms.html">microorganisms$fullname</a></code> and must have a reference column with your own defined values. If all tests pass, <code>set_mo_source()</code> will read the file into <span style="R">R</span> and will ask to export it to <code>"~/mo_source.rds"</code>. The CRAN policy disallows packages to write to the file system, although '<em>exceptions may be allowed in interactive sessions if the package obtains confirmation from the user</em>'. For this reason, this function only works in interactive sessions so that the user can <strong>specifically confirm and allow</strong> that this file will be created. The destination of this file can be set with the <code>destination</code> argument and defaults to the user's home directory. It can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_mo_source</a></code>, e.g. <code>options(AMR_mo_source = "my/location/file.rds")</code>.</p> <p><code>set_mo_source()</code> will check the file for validity: it must be a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, must have a column named <code>"mo"</code> which contains values from <code><a href="microorganisms.html">microorganisms$mo</a></code> or <code><a href="microorganisms.html">microorganisms$fullname</a></code> and must have a reference column with your own defined values. If all tests pass, <code>set_mo_source()</code> will read the file into <span style="R">R</span> and will ask to export it to <code>"~/mo_source.rds"</code>. The CRAN policy disallows packages to write to the file system, although '<em>exceptions may be allowed in interactive sessions if the package obtains confirmation from the user</em>'. For this reason, this function only works in interactive sessions so that the user can <strong>specifically confirm and allow</strong> that this file will be created. The destination of this file can be set with the <code>destination</code> argument and defaults to the user's home directory. It can also be set with the package option <code><a href="AMR-options.html">AMR_mo_source</a></code>, e.g. <code>options(AMR_mo_source = "my/location/file.rds")</code>.</p>
<p>The created compressed data file <code>"mo_source.rds"</code> will be used at default for MO determination (function <code><a href="as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions like <code><a href="mo_property.html">mo_genus()</a></code> and <code><a href="mo_property.html">mo_gramstain()</a></code>). The location and timestamp of the original file will be saved as an <a href="https://rdrr.io/r/base/attributes.html" class="external-link">attribute</a> to the compressed data file.</p> <p>The created compressed data file <code>"mo_source.rds"</code> will be used at default for MO determination (function <code><a href="as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions like <code><a href="mo_property.html">mo_genus()</a></code> and <code><a href="mo_property.html">mo_gramstain()</a></code>). The location and timestamp of the original file will be saved as an <a href="https://rdrr.io/r/base/attributes.html" class="external-link">attribute</a> to the compressed data file.</p>
<p>The function <code>get_mo_source()</code> will return the data set by reading <code>"mo_source.rds"</code> with <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS()</a></code>. If the original file has changed (by checking the location and timestamp of the original file), it will call <code>set_mo_source()</code> to update the data file automatically if used in an interactive session.</p> <p>The function <code>get_mo_source()</code> will return the data set by reading <code>"mo_source.rds"</code> with <code><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS()</a></code>. If the original file has changed (by checking the location and timestamp of the original file), it will call <code>set_mo_source()</code> to update the data file automatically if used in an interactive session.</p>
<p>Reading an Excel file (<code>.xlsx</code>) with only one row has a size of 8-9 kB. The compressed file created with <code>set_mo_source()</code> will then have a size of 0.1 kB and can be read by <code>get_mo_source()</code> in only a couple of microseconds (millionths of a second).</p> <p>Reading an Excel file (<code>.xlsx</code>) with only one row has a size of 8-9 kB. The compressed file created with <code>set_mo_source()</code> will then have a size of 0.1 kB and can be read by <code>get_mo_source()</code> in only a couple of microseconds (millionths of a second).</p>

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reference/pca.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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@ -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> <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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -51,7 +51,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<div class="row"> <div class="row">
<main id="main" class="col-md-9"><div class="page-header"> <main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Plotting for Classes <code>sir</code>, <code>mic</code> and <code>disk</code></h1> <img src="../logo.svg" class="logo" alt=""><h1>Plotting for Classes <code>sir</code>, <code>mic</code> and <code>disk</code></h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/plot.R" class="external-link"><code>R/plot.R</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/plotting.R" class="external-link"><code>R/plotting.R</code></a></small>
<div class="d-none name"><code>plot.Rd</code></div> <div class="d-none name"><code>plot.Rd</code></div>
</div> </div>
@ -218,7 +218,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt> <dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
<dd><p>language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant' - the default is system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can be overwritten by setting the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>, e.g. <code>options(AMR_locale = "de")</code>, see <a href="translate.html">translate</a>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd> <dd><p>language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant' - the default is system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can be overwritten by setting the package option <code><a href="AMR-options.html">AMR_locale</a></code>, e.g. <code>options(AMR_locale = "de")</code>, see <a href="translate.html">translate</a>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt id="arg-expand">expand<a class="anchor" aria-label="anchor" href="#arg-expand"></a></dt> <dt id="arg-expand">expand<a class="anchor" aria-label="anchor" href="#arg-expand"></a></dt>
@ -226,11 +226,11 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<dt id="arg-include-pkpd">include_PKPD<a class="anchor" aria-label="anchor" href="#arg-include-pkpd"></a></dt> <dt id="arg-include-pkpd">include_PKPD<a class="anchor" aria-label="anchor" href="#arg-include-pkpd"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is <code>TRUE</code>. Can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_include_PKPD</a></code>.</p></dd> <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is <code>TRUE</code>. Can also be set with the package option <code><a href="AMR-options.html">AMR_include_PKPD</a></code>.</p></dd>
<dt id="arg-breakpoint-type">breakpoint_type<a class="anchor" aria-label="anchor" href="#arg-breakpoint-type"></a></dt> <dt id="arg-breakpoint-type">breakpoint_type<a class="anchor" aria-label="anchor" href="#arg-breakpoint-type"></a></dt>
<dd><p>the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is <code>"human"</code>, which can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>. If <code>host</code> is set to values of veterinary species, this will automatically be set to <code>"animal"</code>.</p></dd> <dd><p>the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is <code>"human"</code>, which can also be set with the package option <code><a href="AMR-options.html">AMR_breakpoint_type</a></code>. If <code>host</code> is set to values of veterinary species, this will automatically be set to <code>"animal"</code>.</p></dd>
</dl></div> </dl></div>
<div class="section level2"> <div class="section level2">
@ -270,7 +270,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-in"><span><span class="co"># Plotting using scale_x_mic()</span></span></span> <span class="r-in"><span><span class="co"># Plotting using scale_x_mic()</span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span> <span class="r-in"><span><span class="co"># \donttest{</span></span></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">)</span> <span class="op">{</span></span></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">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">mic_plot</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mics <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><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">0.125</span>, <span class="st">"&lt;=4"</span>, <span class="fl">4</span>, <span class="fl">8</span>, <span class="fl">32</span>, <span class="st">"&gt;=32"</span><span class="op">)</span><span class="op">)</span>,</span></span> <span class="r-in"><span> <span class="va">mic_plot</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mics <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><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">0.25</span>, <span class="st">"&lt;=4"</span>, <span class="fl">4</span>, <span class="fl">8</span>, <span class="fl">32</span>, <span class="st">"&gt;=32"</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> counts <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">1</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span>,</span></span> <span class="r-in"><span> counts <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">1</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="va">mics</span>, <span class="va">counts</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="va">mics</span>, <span class="va">counts</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link">geom_col</a></span><span class="op">(</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link">geom_col</a></span><span class="op">(</span><span class="op">)</span></span></span>
@ -292,23 +292,29 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-plt img"><img src="plot-9.png" alt="" width="700" height="433"></span> <span class="r-plt img"><img src="plot-9.png" alt="" width="700" height="433"></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">)</span> <span class="op">{</span></span></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">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">mic_plot</span> <span class="op">+</span></span></span> <span class="r-in"><span> <span class="va">mic_plot</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_x_mic</span><span class="op">(</span>mic_range <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">1</span>, <span class="fl">128</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span> <span class="r-in"><span> <span class="fu">scale_x_mic</span><span class="op">(</span>mic_range <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">1</span>, <span class="fl">16</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic() using a manual range"</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic() using a manual 'within' range"</span><span class="op">)</span></span></span>
<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-plt img"><img src="plot-10.png" alt="" width="700" height="433"></span> <span class="r-plt img"><img src="plot-10.png" alt="" width="700" height="433"></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">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">mic_plot</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_x_mic</span><span class="op">(</span>mic_range <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">0.032</span>, <span class="fl">256</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic() using a manual 'outside' range"</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="plot-11.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span> <span class="r-in"><span></span></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">)</span> <span class="op">{</span></span></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">)</span> <span class="op">{</span></span></span>
<span class="r-in"><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">some_mic_values</span><span class="op">)</span></span></span> <span class="r-in"><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">some_mic_values</span><span class="op">)</span></span></span>
<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-plt img"><img src="plot-11.png" alt="" width="700" height="433"></span> <span class="r-plt img"><img src="plot-12.png" alt="" width="700" height="433"></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">)</span> <span class="op">{</span></span></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">)</span> <span class="op">{</span></span></span>
<span class="r-in"><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">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span> <span class="r-in"><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">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
<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-plt img"><img src="plot-12.png" alt="" width="700" height="433"></span> <span class="r-plt img"><img src="plot-13.png" alt="" width="700" height="433"></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">)</span> <span class="op">{</span></span></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">)</span> <span class="op">{</span></span></span>
<span class="r-in"><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">some_sir_values</span><span class="op">)</span></span></span> <span class="r-in"><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">some_sir_values</span><span class="op">)</span></span></span>
<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-plt img"><img src="plot-13.png" alt="" width="700" height="433"></span> <span class="r-plt img"><img src="plot-14.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div> </code></pre></div>
</div> </div>

4
reference/proportion.html
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> <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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -157,7 +157,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt> <dt id="arg-language">language<a class="anchor" aria-label="anchor" href="#arg-language"></a></dt>
<dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd> <dd><p>language of the returned text - the default is the current system language (see <code><a href="translate.html">get_AMR_locale()</a></code>) and can also be set with the package option <code><a href="AMR-options.html">AMR_locale</a></code>. Use <code>language = NULL</code> or <code>language = ""</code> to prevent translation.</p></dd>
<dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt> <dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt>

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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/skewness.html
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@ -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> <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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

8
reference/translate.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</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="">2.1.1.9078</small> <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9080</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"> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -83,7 +83,7 @@
<div class="section level2"> <div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>The currently 20 supported languages are English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), and Ukrainian (uk). All these languages have translations available for all antimicrobial drugs and colloquial microorganism names.</p> <p>The currently 20 supported languages are English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), and Ukrainian (uk). All these languages have translations available for all antimicrobial drugs and colloquial microorganism names.</p>
<p>To permanently silence the once-per-session language note on a non-English operating system, you can set the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code> in your <code>.Rprofile</code> file like this:</p> <p>To permanently silence the once-per-session language note on a non-English operating system, you can set the package option <code><a href="AMR-options.html">AMR_locale</a></code> in your <code>.Rprofile</code> file like this:</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="co"># Open .Rprofile file</span></span> <p></p><div class="sourceCode r"><pre><code><span><span class="co"># Open .Rprofile file</span></span>
<span><span class="fu">utils</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/utils/file.edit.html" class="external-link">file.edit</a></span><span class="op">(</span><span class="st">"~/.Rprofile"</span><span class="op">)</span></span> <span><span class="fu">utils</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/utils/file.edit.html" class="external-link">file.edit</a></span><span class="op">(</span><span class="st">"~/.Rprofile"</span><span class="op">)</span></span>
<span></span> <span></span>
@ -94,10 +94,10 @@
<h3 id="changing-the-default-language">Changing the Default Language<a class="anchor" aria-label="anchor" href="#changing-the-default-language"></a></h3> <h3 id="changing-the-default-language">Changing the Default Language<a class="anchor" aria-label="anchor" href="#changing-the-default-language"></a></h3>
<p>The system language will be used at default (as returned by <code>Sys.getenv("LANG")</code> or, if <code>LANG</code> is not set, <code><a href="https://rdrr.io/r/base/locales.html" class="external-link">Sys.getlocale("LC_COLLATE")</a></code>), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:</p><ol><li><p>Setting the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code>, either by using e.g. <code>set_AMR_locale("German")</code> or by running e.g. <code>options(AMR_locale = "German")</code>.</p> <p>The system language will be used at default (as returned by <code>Sys.getenv("LANG")</code> or, if <code>LANG</code> is not set, <code><a href="https://rdrr.io/r/base/locales.html" class="external-link">Sys.getlocale("LC_COLLATE")</a></code>), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:</p><ol><li><p>Setting the package option <code><a href="AMR-options.html">AMR_locale</a></code>, either by using e.g. <code>set_AMR_locale("German")</code> or by running e.g. <code>options(AMR_locale = "German")</code>.</p>
<p>Note that setting an <span style="R">R</span> option only works in the same session. Save the command <code>options(AMR_locale = "(your language)")</code> to your <code>.Rprofile</code> file to apply it for every session. Run <code>utils::file.edit("~/.Rprofile")</code> to edit your <code>.Rprofile</code> file.</p></li> <p>Note that setting an <span style="R">R</span> option only works in the same session. Save the command <code>options(AMR_locale = "(your language)")</code> to your <code>.Rprofile</code> file to apply it for every session. Run <code>utils::file.edit("~/.Rprofile")</code> to edit your <code>.Rprofile</code> file.</p></li>
<li><p>Setting the system variable <code>LANGUAGE</code> or <code>LANG</code>, e.g. by adding <code>LANGUAGE="de_DE.utf8"</code> to your <code>.Renviron</code> file in your home directory.</p></li> <li><p>Setting the system variable <code>LANGUAGE</code> or <code>LANG</code>, e.g. by adding <code>LANGUAGE="de_DE.utf8"</code> to your <code>.Renviron</code> file in your home directory.</p></li>
</ol><p>Thus, if the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_locale</a></code> is set, the system variables <code>LANGUAGE</code> and <code>LANG</code> will be ignored.</p> </ol><p>Thus, if the package option <code><a href="AMR-options.html">AMR_locale</a></code> is set, the system variables <code>LANGUAGE</code> and <code>LANG</code> will be ignored.</p>
</div> </div>
</div> </div>

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