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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="">3.0.0.9033</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9034</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">
@@ -188,8 +188,8 @@
<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: #080808;"> is </span><span style="color: #080808; background-color: #FFAFAF;"> R </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">age</span><span style="color: #080808;"> 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: #080808;"> is </span><span style="color: #080808; background-color: #FFAFAF;"> R </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">age</span><span style="color: #080808;"> 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> 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>
@@ -233,8 +233,8 @@
<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: #080808;"> is </span><span style="color: #080808; background-color: #FFAFAF;"> 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: #080808;">all of </span><span style="color: #0000BB;">cephalosporins_2nd()</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FFAFAF;"> 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> 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>
@@ -249,10 +249,10 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> it seems to be lenampicillin (LEN)</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Column '</span><span style="color: #0000BB; font-weight: bold;">vanB</span><span style="color: #0000BB;">' is SIR eligible (despite only having empty values), since</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> it seems to be metronidazole (MTR)</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`cephalosporins_2nd()`</span><span style="color: #0000BB;"> 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;">ℹ For </span><span style="color: #0000BB; background-color: #444444;">`cephalosporins_2nd()`</span><span style="color: #0000BB;"> 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 </span><span style="color: #0000BB; background-color: #EEEEEE;">`all()`</span><span style="color: #0000BB;"> or</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> </span><span style="color: #0000BB; background-color: #EEEEEE;">`any()`</span><span style="color: #0000BB;"> to prevent this note.</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 </span><span style="color: #0000BB; background-color: #444444;">`all()`</span><span style="color: #0000BB;"> or</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> </span><span style="color: #0000BB; background-color: #444444;">`any()`</span><span style="color: #0000BB;"> to prevent this note.</span></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>