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Built site for AMR: 2.0.0.9005@147f911

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2023-04-14 09:23:10 +00:00
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commit cc245a41a0
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reference/custom_eucast_rules.html
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@ -10,7 +10,7 @@
<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="">2.0.0.9004</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9005</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">
@ -276,17 +276,16 @@
<span class="r-in"><span> verbose <span class="op">=</span> <span class="cn">TRUE</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 8 × 9</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> row col mo_fullname old new rule rule_…¹ rule_…² rule_…³</span>
<span class="r-out co"><span class="r-pr">#&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;ord&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 33 AMP Klebsiella pneumoniae R I <span style="color: #949494;">"</span>report… Custom… Custom… Object…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 33 AMX Klebsiella pneumoniae R I <span style="color: #949494;">"</span>report… Custom… Custom… Object…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 34 AMP Klebsiella pneumoniae R I <span style="color: #949494;">"</span>report… Custom… Custom… Object…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 34 AMX Klebsiella pneumoniae R I <span style="color: #949494;">"</span>report… Custom… Custom… Object…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> 531 AMP Klebsiella pneumoniae R I <span style="color: #949494;">"</span>report… Custom… Custom… Object…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> 531 AMX Klebsiella pneumoniae R I <span style="color: #949494;">"</span>report… Custom… Custom… Object…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">7</span> <span style="text-decoration: underline;">1</span>485 AMP Klebsiella oxytoca R I <span style="color: #949494;">"</span>report… Custom… Custom… Object…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">8</span> <span style="text-decoration: underline;">1</span>485 AMX Klebsiella oxytoca R I <span style="color: #949494;">"</span>report… Custom… Custom… Object…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with abbreviated variable names ¹​rule_group, ²​rule_name, ³​rule_source</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> row col mo_fullname old new rule rule_group rule_name rule_source</span>
<span class="r-out co"><span class="r-pr">#&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;ord&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 33 AMP Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 33 AMX Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 34 AMP Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 34 AMX Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> 531 AMP Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> 531 AMX Klebsiella pne… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">7</span> <span style="text-decoration: underline;">1</span>485 AMP Klebsiella oxy… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">8</span> <span style="text-decoration: underline;">1</span>485 AMX Klebsiella oxy… R I <span style="color: #949494;">"</span>rep… Custom EU… Custom E… Object 'x'…</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># combine rule sets</span></span></span>
<span class="r-in"><span><span class="va">x2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>