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@ -32,7 +32,7 @@
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">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">
@ -92,7 +92,7 @@
<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>
<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>Integrates with <strong>WHONET</strong>, ATC, <strong>EARS-Net</strong>, PubChem, <strong>LOINC</strong>, <strong>SNOMED CT</strong>, and <strong>NCBI</strong>
</li>
@ -267,115 +267,115 @@
<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>
<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">
<th align="left">Pathogen (N min-max)</th>
<th align="right">AMK</th>
<th align="right">GEN</th>
<th align="right">IPM</th>
<th align="right">KAN</th>
<th align="right">MEM</th>
<th align="right">TOB</th>
<th align="left">Pathogen</th>
<th align="center">Amikacin</th>
<th align="center">Gentamicin</th>
<th align="center">Imipenem</th>
<th align="center">Kanamycin</th>
<th align="center">Meropenem</th>
<th align="center">Tobramycin</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">CoNS (43-309)</td>
<td align="right">0</td>
<td align="right">86</td>
<td align="right">52</td>
<td align="right">0</td>
<td align="right">52</td>
<td align="right">22</td>
<td align="left">CoNS</td>
<td align="center">0% (0/43)</td>
<td align="center">86% (267/309)</td>
<td align="center">52% (25/48)</td>
<td align="center">0% (0/43)</td>
<td align="center">52% (25/48)</td>
<td align="center">22% (12/55)</td>
</tr>
<tr class="even">
<td align="left">
<em>E. coli</em> (0-462)</td>
<td align="right">100</td>
<td align="right">98</td>
<td align="right">100</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right">97</td>
<td align="left"><em>E. coli</em></td>
<td align="center">100% (171/171)</td>
<td align="center">98% (451/460)</td>
<td align="center">100% (422/422)</td>
<td align="center"></td>
<td align="center">100% (418/418)</td>
<td align="center">97% (450/462)</td>
</tr>
<tr class="odd">
<td align="left">
<em>E. faecalis</em> (0-39)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">100</td>
<td align="right">0</td>
<td align="right"></td>
<td align="right">0</td>
<td align="left"><em>E. faecalis</em></td>
<td align="center">0% (0/39)</td>
<td align="center">0% (0/39)</td>
<td align="center">100% (38/38)</td>
<td align="center">0% (0/39)</td>
<td align="center"></td>
<td align="center">0% (0/39)</td>
</tr>
<tr class="even">
<td align="left">
<em>K. pneumoniae</em> (0-58)</td>
<td align="right"></td>
<td align="right">90</td>
<td align="right">100</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right">90</td>
<td align="left"><em>K. pneumoniae</em></td>
<td align="center"></td>
<td align="center">90% (52/58)</td>
<td align="center">100% (51/51)</td>
<td align="center"></td>
<td align="center">100% (53/53)</td>
<td align="center">90% (52/58)</td>
</tr>
<tr class="odd">
<td align="left">
<em>P. aeruginosa</em> (17-30)</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right"></td>
<td align="right">0</td>
<td align="right"></td>
<td align="right">100</td>
<td align="left"><em>P. aeruginosa</em></td>
<td align="center"></td>
<td align="center">100% (30/30)</td>
<td align="center"></td>
<td align="center">0% (0/30)</td>
<td align="center"></td>
<td align="center">100% (30/30)</td>
</tr>
<tr class="even">
<td align="left">
<em>P. mirabilis</em> (0-34)</td>
<td align="right"></td>
<td align="right">94</td>
<td align="right">94</td>
<td align="right"></td>
<td align="right"></td>
<td align="right">94</td>
<td align="left"><em>P. mirabilis</em></td>
<td align="center"></td>
<td align="center">94% (32/34)</td>
<td align="center">94% (30/32)</td>
<td align="center"></td>
<td align="center"></td>
<td align="center">94% (32/34)</td>
</tr>
<tr class="odd">
<td align="left">
<em>S. aureus</em> (2-233)</td>
<td align="right"></td>
<td align="right">99</td>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
<td align="right">98</td>
<td align="left"><em>S. aureus</em></td>
<td align="center"></td>
<td align="center">99% (231/233)</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">98% (84/86)</td>
</tr>
<tr class="even">
<td align="left">
<em>S. epidermidis</em> (8-163)</td>
<td align="right">0</td>
<td align="right">79</td>
<td align="right"></td>
<td align="right">0</td>
<td align="right"></td>
<td align="right">51</td>
<td align="left"><em>S. epidermidis</em></td>
<td align="center">0% (0/44)</td>
<td align="center">79% (128/163)</td>
<td align="center"></td>
<td align="center">0% (0/44)</td>
<td align="center"></td>
<td align="center">51% (45/89)</td>
</tr>
<tr class="odd">
<td align="left">
<em>S. hominis</em> (3-80)</td>
<td align="right"></td>
<td align="right">92</td>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
<td align="right">85</td>
<td align="left"><em>S. hominis</em></td>
<td align="center"></td>
<td align="center">92% (74/80)</td>
<td align="center"></td>
<td align="center"></td>
<td align="center"></td>
<td align="center">85% (53/62)</td>
</tr>
<tr class="even">
<td align="left">
<em>S. pneumoniae</em> (11-117)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right"></td>
<td align="right">0</td>
<td align="right"></td>
<td align="right">0</td>
<td align="left"><em>S. pneumoniae</em></td>
<td align="center">0% (0/117)</td>
<td align="center">0% (0/117)</td>
<td align="center"></td>
<td align="center">0% (0/117)</td>
<td align="center"></td>
<td align="center">0% (0/117)</td>
</tr>
</tbody>
</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> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="12%">
<col width="21%">
<col width="33%">
<col width="32%">
</colgroup>
<thead><tr class="header">
<th align="left">Pathogen (N min-max)</th>
<th align="right">TZP</th>
<th align="right">TZP + GEN</th>
<th align="right">TZP + TOB</th>
<th align="left">Pathogen</th>
<th align="center">Piperacillin/tazobactam</th>
<th align="center">Piperacillin/tazobactam + Gentamicin</th>
<th align="center">Piperacillin/tazobactam + Tobramycin</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Gram-negative (641-693)</td>
<td align="right">88</td>
<td align="right">99</td>
<td align="right">98</td>
<td align="left">Gram-negative</td>
<td align="center">88% (565/641)</td>
<td align="center">99% (681/691)</td>
<td align="center">98% (679/693)</td>
</tr>
<tr class="even">
<td align="left">Gram-positive (345-1044)</td>
<td align="right">86</td>
<td align="right">98</td>
<td align="right">95</td>
<td align="left">Gram-positive</td>
<td align="center">86% (296/345)</td>
<td align="center">98% (1018/1044)</td>
<td align="center">95% (524/550)</td>
</tr>
</tbody>
</table>
@ -414,24 +420,30 @@
<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>
<table class="table">
<colgroup>
<col width="20%">
<col width="27%">
<col width="26%">
<col width="25%">
</colgroup>
<thead><tr class="header">
<th align="left">Збудник (N min-max)</th>
<th align="right">Гентаміцин</th>
<th align="right">Тобраміцин</th>
<th align="right">Ципрофлоксацин</th>
<th align="left">Збудник</th>
<th align="center">Гентаміцин</th>
<th align="center">Тобраміцин</th>
<th align="center">Ципрофлоксацин</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Грамнегативні (684-686)</td>
<td align="right">96</td>
<td align="right">96</td>
<td align="right">91</td>
<td align="left">Грамнегативні</td>
<td align="center">96% (659/684)</td>
<td align="center">96% (658/686)</td>
<td align="center">91% (621/684)</td>
</tr>
<tr class="even">
<td align="left">Грампозитивні (665-1170)</td>
<td align="right">63</td>
<td align="right">34</td>
<td align="right">77</td>
<td align="left">Грампозитивні</td>
<td align="center">63% (740/1170)</td>
<td align="center">34% (228/665)</td>
<td align="center">77% (560/724)</td>
</tr>
</tbody>
</table>