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2026-03-20 16:11:30 +00:00
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reference/custom_mdro_guideline.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9035</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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">
@@ -192,9 +192,9 @@
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> A set of custom MDRO rules:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">CIP</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #BBBBBB; font-weight: bold;"> and </span><span style="color: #0000BB;">age</span><span style="color: #BBBBBB;"> is higher than </span><span style="color: #0000BB;">60</span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Elderly Type A</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">ERY</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #BBBBBB; font-weight: bold;"> and </span><span style="color: #0000BB;">age</span><span style="color: #BBBBBB;"> is higher than </span><span style="color: #0000BB;">60</span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Elderly Type B</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3. <span style="font-weight: bold;">Otherwise: </span><span style="color: #BB0000;">Negative</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">CIP</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #BBBBBB; font-weight: bold;"> and </span><span style="color: #0000BB;">age</span><span style="color: #BBBBBB;"> is higher than </span><span style="color: #0000BB;">60</span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Elderly Type A</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   2. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">ERY</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #BBBBBB; font-weight: bold;"> and </span><span style="color: #0000BB;">age</span><span style="color: #BBBBBB;"> is higher than </span><span style="color: #0000BB;">60</span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Elderly Type B</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   3. <span style="font-weight: bold;">Otherwise: </span><span style="color: #BB0000;">Negative</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Unmatched rows will return <span style="color: #BB0000;">NA</span>.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Results will be of class 'factor', with ordered levels: Negative &lt; Elderly Type A &lt; Elderly Type B</span>
@@ -237,18 +237,18 @@
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">my_guideline</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> A set of custom MDRO rules:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMX</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Custom MDRO 1</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2. <span style="font-weight: bold;">If </span><span style="color: #BBBBBB;">all of </span><span style="color: #0000BB;">cephalosporins_2nd()</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Custom MDRO 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3. <span style="font-weight: bold;">Otherwise: </span><span style="color: #BB0000;">Negative</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMX</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Custom MDRO 1</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   2. <span style="font-weight: bold;">If </span><span style="color: #BBBBBB;">all of </span><span style="color: #0000BB;">cephalosporins_2nd()</span><span style="color: #BBBBBB;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Custom MDRO 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   3. <span style="font-weight: bold;">Otherwise: </span><span style="color: #BB0000;">Negative</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Unmatched rows will return <span style="color: #BB0000;">NA</span>.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Results will be of class 'factor', with ordered levels: Negative &lt; Custom MDRO 1 &lt; Custom MDRO 2</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">out</span> <span class="op">&lt;-</span> <span class="fu"><a href="mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">my_guideline</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For `cephalosporins_2nd()` using columns '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">' (cefuroxime) and '</span><span style="color: #0000BB; font-weight: bold;">FOX</span><span style="color: #0000BB;">'</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (cefoxitin)</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Assuming a filter on all 2 cephalosporins_2nd. Wrap around `all()` or</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> `any()` to prevent this note.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> For `cephalosporins_2nd()` using columns '<span style="font-weight: bold;">CXM</span>' (cefuroxime) and '<span style="font-weight: bold;">FOX</span>'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (cefoxitin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Assuming a filter on all 2 cephalosporins_2nd. Wrap around `all()` or `any()`</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> to prevent this note.</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">out</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> out</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Negative Custom MDRO 1 Custom MDRO 2 </span>